CryoREAD is a computational tool using deep learning to automatically build full DNA/RNA atomic
structure from cryo-EM map at resolution 0-5A.
It outputs a file in .pdb format that records the modeled DNA/RNA structure from the input cryo-EM
map.
For cryo-EM map includes proteins, it only modeled the DNA/RNA structures in the complex.
If you want to model the full complex, please try
ComplexModeler(https://em.kiharalab.org/algorithm/ComplexModeler).
Our results webpage comprises three tabs: Results Visualization, Output Logs, and Job Configuration.
Results Visualization:
The "Result Visualization" panel contains the DNA/RNA structure modeled by CryoREAD.
In the right panel, you can also click "Download Outputs" button to download the modeled structure.
The downloaded structure is in .pdb format, you can use PyMol/Coot/Chimera to visualize it or refine
it based on your expertise.
Additionally, you can visualize the map online by clicking the "Show map" button.
Once loaded, the default contour level matches your input; however, you can make adjustments by
clicking the "..." button beside "isosurface."
Within the "Type: Isosurface" option, you can modify the iso-surface value and opacity by scrolling
through the bar for precise adjustments.
This feature allows you to assess the alignment between the modeled structure and the map.
Output Logs:
The 'Output Logs' panel compiles all outputs generated by the scripts.
If you're interested in monitoring the job's progress during execution, this section provides a
comprehensive overview.
Job Configuration:
In the 'Job Configuration' panel, you'll find the input parameters used for this specific job.
These records serve to maintain a log of your submitted input for reference.
Problem Debugging:
For any troubleshooting needs: Should you encounter any issues, please don't hesitate to contact us
via
email to report the problems.
When sending an email, kindly use the subject line format 'CryoREAD problem: [jobid]', where [jobid]
corresponds to the job displayed in the title.
This specific identification helps us efficiently locate and debug jobs in the backend, ensuring a
prompt response to your concerns.
Contact:
dkihara@purdue.edu, xiaowang20140001@gmail.com.
CryoREAD
Job ID : 10043363bd0b413a007d1f8f2150caf7
CryoREAD is a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map (2-5A). It can handle DNA/RNA-only and DNA/RNA-protein complex map. If you encounter any questions for the modeled structure, feel free to email dkihara@purdue.edu and wang3702@purdue.edu!
CryoREAD (no sequence version) started
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/ existed
Origin: (0., 0., 0.)
Previous voxel size: 1.059999942779541
Previouse size: (256, 256, 256) Current map size: 271 271 271
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nz : 256
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my : 256
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cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.247260093688965
dmax : 3.386734962463379
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/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/1st_stage_detection created
map density range: 0.000000 3.159605
map hist log percentage 98: 2.5908763
detected mode mapc 1, mapr 2, maps 3
Origin: [0.0, 0.0, 0.0]
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/1st_stage_detection/Input created
given contour 0.300000
revised contour 0.115791
In total we prepared 1103 boxes as input
model loading: <All keys matched successfully>
#Eval:[ 0/276] data_time 0.168809 (0.168809) train_time 1.388435 (1.388435)
0 classes already detected 15 voxels
1 classes already detected 0 voxels
2 classes already detected 0 voxels
3 classes already detected 3810 voxels
#Eval:[ 1/276] data_time 0.001800 (0.085305) train_time 1.142597 (1.265516)
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#Eval:[115/276] data_time 0.001632 (0.002941) train_time 1.649377 (1.417384)
#Eval:[116/276] data_time 0.001682 (0.002930) train_time 1.665218 (1.419502)
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#Eval:[122/276] data_time 0.001428 (0.002861) train_time 1.645391 (1.430678)
#Eval:[123/276] data_time 0.001395 (0.002849) train_time 1.650068 (1.432448)
#Eval:[124/276] data_time 0.001464 (0.002838) train_time 1.651278 (1.434198)
#Eval:[125/276] data_time 0.001480 (0.002827) train_time 1.646598 (1.435884)
#Eval:[126/276] data_time 0.001454 (0.002816) train_time 1.647682 (1.437552)
#Eval:[127/276] data_time 0.001546 (0.002806) train_time 1.653528 (1.439239)
#Eval:[128/276] data_time 0.001498 (0.002796) train_time 1.645381 (1.440837)
#Eval:[129/276] data_time 0.001564 (0.002787) train_time 1.644861 (1.442407)
#Eval:[130/276] data_time 0.001423 (0.002776) train_time 1.651622 (1.444004)
#Eval:[131/276] data_time 0.001677 (0.002768) train_time 1.652293 (1.445582)
#Eval:[132/276] data_time 0.001357 (0.002757) train_time 1.650806 (1.447125)
#Eval:[133/276] data_time 0.001448 (0.002748) train_time 1.649523 (1.448635)
#Eval:[134/276] data_time 0.001496 (0.002738) train_time 1.646289 (1.450099)
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#Eval:[136/276] data_time 0.001486 (0.002720) train_time 1.646991 (1.453024)
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#Eval:[138/276] data_time 0.001475 (0.002702) train_time 1.652427 (1.455860)
#Eval:[139/276] data_time 0.001481 (0.002693) train_time 1.649833 (1.457245)
#Eval:[140/276] data_time 0.001468 (0.002684) train_time 1.648769 (1.458604)
#Eval:[141/276] data_time 0.001275 (0.002675) train_time 1.650670 (1.459956)
#Eval:[142/276] data_time 0.001900 (0.002669) train_time 1.647097 (1.461265)
#Eval:[143/276] data_time 0.001666 (0.002662) train_time 1.650956 (1.462582)
#Eval:[144/276] data_time 0.001436 (0.002654) train_time 1.655115 (1.463910)
#Eval:[145/276] data_time 0.001449 (0.002645) train_time 1.646806 (1.465163)
#Eval:[146/276] data_time 0.001501 (0.002638) train_time 1.648988 (1.466413)
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#Eval:[149/276] data_time 0.001454 (0.002617) train_time 1.650058 (1.470115)
#Eval:[150/276] data_time 0.001518 (0.002609) train_time 1.656691 (1.471350)
#Eval:[151/276] data_time 0.001713 (0.002603) train_time 1.648989 (1.472519)
#Eval:[152/276] data_time 0.001395 (0.002595) train_time 1.645002 (1.473646)
#Eval:[153/276] data_time 0.001235 (0.002587) train_time 1.655208 (1.474825)
#Eval:[154/276] data_time 0.001450 (0.002579) train_time 1.643351 (1.475913)
#Eval:[155/276] data_time 0.001485 (0.002572) train_time 1.651629 (1.477039)
#Eval:[156/276] data_time 0.001678 (0.002567) train_time 1.653109 (1.478160)
#Eval:[157/276] data_time 0.001486 (0.002560) train_time 1.647948 (1.479235)
#Eval:[158/276] data_time 0.001636 (0.002554) train_time 1.650551 (1.480312)
#Eval:[159/276] data_time 0.001448 (0.002547) train_time 1.654900 (1.481404)
#Eval:[160/276] data_time 0.001483 (0.002540) train_time 1.650470 (1.482454)
#Eval:[161/276] data_time 0.001475 (0.002534) train_time 1.651929 (1.483500)
#Eval:[162/276] data_time 0.001525 (0.002528) train_time 1.651984 (1.484533)
#Eval:[163/276] data_time 0.001683 (0.002523) train_time 1.654110 (1.485568)
#Eval:[164/276] data_time 0.001493 (0.002516) train_time 1.643530 (1.486525)
#Eval:[165/276] data_time 0.001452 (0.002510) train_time 1.648796 (1.487502)
#Eval:[166/276] data_time 0.001556 (0.002504) train_time 1.658563 (1.488527)
#Eval:[167/276] data_time 0.001614 (0.002499) train_time 1.656322 (1.489525)
#Eval:[168/276] data_time 0.001623 (0.002494) train_time 1.655312 (1.490506)
#Eval:[169/276] data_time 0.001389 (0.002487) train_time 1.654980 (1.491474)
#Eval:[170/276] data_time 0.001582 (0.002482) train_time 1.659694 (1.492458)
#Eval:[171/276] data_time 0.001486 (0.002476) train_time 1.654384 (1.493399)
#Eval:[172/276] data_time 0.001383 (0.002470) train_time 1.656315 (1.494341)
#Eval:[173/276] data_time 0.001378 (0.002464) train_time 1.658087 (1.495282)
#Eval:[174/276] data_time 0.001498 (0.002458) train_time 1.662695 (1.496239)
#Eval:[175/276] data_time 0.001540 (0.002453) train_time 1.650927 (1.497117)
#Eval:[176/276] data_time 0.001642 (0.002448) train_time 1.656047 (1.498015)
#Eval:[177/276] data_time 0.001482 (0.002443) train_time 1.659915 (1.498925)
#Eval:[178/276] data_time 0.001479 (0.002437) train_time 1.654346 (1.499793)
#Eval:[179/276] data_time 0.001504 (0.002432) train_time 1.657459 (1.500669)
#Eval:[180/276] data_time 0.001498 (0.002427) train_time 1.653902 (1.501516)
#Eval:[181/276] data_time 0.001482 (0.002422) train_time 1.658445 (1.502378)
#Eval:[182/276] data_time 0.001651 (0.002418) train_time 1.655147 (1.503213)
#Eval:[183/276] data_time 0.001519 (0.002413) train_time 1.654359 (1.504034)
#Eval:[184/276] data_time 0.001683 (0.002409) train_time 1.656559 (1.504859)
#Eval:[185/276] data_time 0.001453 (0.002404) train_time 1.657841 (1.505681)
#Eval:[186/276] data_time 0.001521 (0.002399) train_time 1.651058 (1.506459)
#Eval:[187/276] data_time 0.001615 (0.002395) train_time 1.670264 (1.507330)
#Eval:[188/276] data_time 0.001508 (0.002390) train_time 1.669309 (1.508187)
#Eval:[189/276] data_time 0.001513 (0.002385) train_time 1.660786 (1.508990)
#Eval:[190/276] data_time 0.001613 (0.002381) train_time 1.655097 (1.509755)
#Eval:[191/276] data_time 0.001670 (0.002378) train_time 1.657459 (1.510524)
#Eval:[192/276] data_time 0.001852 (0.002375) train_time 1.659244 (1.511295)
#Eval:[193/276] data_time 0.001410 (0.002370) train_time 1.657641 (1.512049)
#Eval:[194/276] data_time 0.001478 (0.002365) train_time 1.655119 (1.512783)
#Eval:[195/276] data_time 0.001644 (0.002362) train_time 1.656252 (1.513515)
#Eval:[196/276] data_time 0.001661 (0.002358) train_time 1.661608 (1.514267)
#Eval:[197/276] data_time 0.001470 (0.002354) train_time 1.661400 (1.515010)
#Eval:[198/276] data_time 0.001535 (0.002350) train_time 1.656368 (1.515720)
#Eval:[199/276] data_time 0.001564 (0.002346) train_time 1.657504 (1.516429)
#Eval:[200/276] data_time 0.001424 (0.002341) train_time 1.657910 (1.517133)
#Eval:[201/276] data_time 0.001456 (0.002337) train_time 1.656127 (1.517821)
#Eval:[202/276] data_time 0.001385 (0.002332) train_time 1.657127 (1.518507)
#Eval:[203/276] data_time 0.001522 (0.002328) train_time 1.658980 (1.519196)
#Eval:[204/276] data_time 0.001471 (0.002324) train_time 1.662282 (1.519894)
#Eval:[205/276] data_time 0.001523 (0.002320) train_time 1.657882 (1.520564)
#Eval:[206/276] data_time 0.001369 (0.002315) train_time 1.656820 (1.521222)
#Eval:[207/276] data_time 0.001465 (0.002311) train_time 1.655184 (1.521866)
#Eval:[208/276] data_time 0.001539 (0.002308) train_time 1.666908 (1.522560)
#Eval:[209/276] data_time 0.001448 (0.002304) train_time 1.662127 (1.523225)
#Eval:[210/276] data_time 0.001401 (0.002299) train_time 1.657174 (1.523859)
#Eval:[211/276] data_time 0.001463 (0.002295) train_time 1.657143 (1.524488)
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#Eval:[214/276] data_time 0.001392 (0.002283) train_time 1.653917 (1.526349)
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#Eval:[216/276] data_time 0.001635 (0.002277) train_time 1.672514 (1.527641)
#Eval:[217/276] data_time 0.001464 (0.002273) train_time 1.664530 (1.528269)
#Eval:[218/276] data_time 0.001467 (0.002270) train_time 1.655067 (1.528848)
#Eval:[219/276] data_time 0.001677 (0.002267) train_time 1.661945 (1.529453)
#Eval:[220/276] data_time 0.001646 (0.002264) train_time 1.656834 (1.530030)
#Eval:[221/276] data_time 0.001476 (0.002261) train_time 1.663105 (1.530629)
#Eval:[222/276] data_time 0.001472 (0.002257) train_time 1.655548 (1.531189)
#Eval:[223/276] data_time 0.001631 (0.002254) train_time 1.654373 (1.531739)
#Eval:[224/276] data_time 0.001636 (0.002252) train_time 1.662595 (1.532321)
#Eval:[225/276] data_time 0.001512 (0.002248) train_time 1.650803 (1.532845)
#Eval:[226/276] data_time 0.001464 (0.002245) train_time 1.656193 (1.533389)
#Eval:[227/276] data_time 0.001501 (0.002242) train_time 1.666062 (1.533970)
#Eval:[228/276] data_time 0.001891 (0.002240) train_time 1.658444 (1.534514)
#Eval:[229/276] data_time 0.001729 (0.002238) train_time 1.654293 (1.535035)
#Eval:[230/276] data_time 0.001492 (0.002235) train_time 1.667166 (1.535607)
#Eval:[231/276] data_time 0.001694 (0.002232) train_time 1.662617 (1.536154)
#Eval:[232/276] data_time 0.001383 (0.002229) train_time 1.653800 (1.536659)
#Eval:[233/276] data_time 0.001744 (0.002227) train_time 1.656768 (1.537172)
#Eval:[234/276] data_time 0.001470 (0.002223) train_time 1.663934 (1.537712)
#Eval:[235/276] data_time 0.001532 (0.002221) train_time 1.660922 (1.538234)
#Eval:[236/276] data_time 0.001334 (0.002217) train_time 1.665404 (1.538770)
#Eval:[237/276] data_time 0.001532 (0.002214) train_time 1.668794 (1.539317)
#Eval:[238/276] data_time 0.001474 (0.002211) train_time 1.661328 (1.539827)
#Eval:[239/276] data_time 0.001722 (0.002209) train_time 1.662391 (1.540338)
#Eval:[240/276] data_time 0.001734 (0.002207) train_time 1.665977 (1.540859)
#Eval:[241/276] data_time 0.001640 (0.002204) train_time 1.661547 (1.541358)
#Eval:[242/276] data_time 0.001989 (0.002204) train_time 1.659326 (1.541843)
#Eval:[243/276] data_time 0.001666 (0.002201) train_time 1.660182 (1.542328)
#Eval:[244/276] data_time 0.001677 (0.002199) train_time 1.663935 (1.542825)
#Eval:[245/276] data_time 0.001685 (0.002197) train_time 1.660343 (1.543303)
#Eval:[246/276] data_time 0.001472 (0.002194) train_time 1.660338 (1.543776)
#Eval:[247/276] data_time 0.001455 (0.002191) train_time 1.656397 (1.544230)
#Eval:[248/276] data_time 0.001646 (0.002189) train_time 1.658560 (1.544690)
#Eval:[249/276] data_time 0.001452 (0.002186) train_time 1.656520 (1.545137)
#Eval:[250/276] data_time 0.001471 (0.002183) train_time 1.659441 (1.545592)
#Eval:[251/276] data_time 0.001731 (0.002181) train_time 1.665085 (1.546067)
#Eval:[252/276] data_time 0.001453 (0.002179) train_time 1.659730 (1.546516)
#Eval:[253/276] data_time 0.001765 (0.002177) train_time 1.662783 (1.546974)
#Eval:[254/276] data_time 0.001503 (0.002174) train_time 1.659745 (1.547416)
#Eval:[255/276] data_time 0.001472 (0.002172) train_time 1.663746 (1.547870)
#Eval:[256/276] data_time 0.001391 (0.002168) train_time 1.657115 (1.548295)
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#Eval:[259/276] data_time 0.002068 (0.002163) train_time 1.655093 (1.549566)
#Eval:[260/276] data_time 0.001668 (0.002161) train_time 1.659128 (1.549985)
#Eval:[261/276] data_time 0.001408 (0.002158) train_time 1.656112 (1.550391)
#Eval:[262/276] data_time 0.001441 (0.002155) train_time 1.655684 (1.550791)
#Eval:[263/276] data_time 0.001647 (0.002153) train_time 1.657723 (1.551196)
#Eval:[264/276] data_time 0.001744 (0.002152) train_time 1.656446 (1.551593)
#Eval:[265/276] data_time 0.001689 (0.002150) train_time 1.663878 (1.552015)
#Eval:[266/276] data_time 0.001483 (0.002148) train_time 1.657180 (1.552409)
#Eval:[267/276] data_time 0.001858 (0.002147) train_time 1.658519 (1.552805)
#Eval:[268/276] data_time 0.001615 (0.002145) train_time 1.657887 (1.553196)
#Eval:[269/276] data_time 0.001712 (0.002143) train_time 1.656958 (1.553580)
#Eval:[270/276] data_time 0.001452 (0.002140) train_time 1.655012 (1.553954)
#Eval:[271/276] data_time 0.001699 (0.002139) train_time 1.655910 (1.554329)
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dmax : 1.0
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/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/2nd_stage_detection created
map density range: 0.000000 3.159605
map hist log percentage 98: 2.5908763
detected mode mapc 1, mapr 2, maps 3
Origin: [0.0, 0.0, 0.0]
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/2nd_stage_detection/Input created
given contour 0.300000
revised contour 0.115791
in 2nd stage, in total we have 900 boxes
model loading: <All keys matched successfully>
#Eval:[ 0/225] data_time 0.353324 (0.353324) train_time 1.021894 (1.021894)
0 classes already detected 724 voxels
1 classes already detected 359 voxels
2 classes already detected 0 voxels
3 classes already detected 2 voxels
4 classes already detected 36 voxels
5 classes already detected 128 voxels
6 classes already detected 29879 voxels
7 classes already detected 935 voxels
#Eval:[ 1/225] data_time 0.222827 (0.288076) train_time 0.898544 (0.960219)
#Eval:[ 2/225] data_time 0.038179 (0.204777) train_time 0.776937 (0.899125)
#Eval:[ 3/225] data_time 0.037856 (0.163047) train_time 0.787261 (0.871159)
#Eval:[ 4/225] data_time 0.040595 (0.138556) train_time 0.791972 (0.855322)
#Eval:[ 5/225] data_time 0.040988 (0.122295) train_time 0.797586 (0.845699)
#Eval:[ 6/225] data_time 0.040360 (0.110590) train_time 0.789036 (0.837604)
#Eval:[ 7/225] data_time 0.039896 (0.101753) train_time 0.791974 (0.831900)
#Eval:[ 8/225] data_time 0.040278 (0.094923) train_time 0.790321 (0.827281)
#Eval:[ 9/225] data_time 0.041770 (0.089607) train_time 0.796901 (0.824243)
#Eval:[ 10/225] data_time 0.040153 (0.085111) train_time 0.792347 (0.821343)
#Eval:[ 11/225] data_time 0.039981 (0.081351) train_time 0.786901 (0.818473)
#Eval:[ 12/225] data_time 0.040867 (0.078236) train_time 0.792876 (0.816504)
#Eval:[ 13/225] data_time 0.040468 (0.075539) train_time 0.798477 (0.815216)
#Eval:[ 14/225] data_time 0.041767 (0.073287) train_time 0.799623 (0.814177)
#Eval:[ 15/225] data_time 0.040311 (0.071226) train_time 0.785644 (0.812393)
#Eval:[ 16/225] data_time 0.040268 (0.069405) train_time 0.797111 (0.811494)
#Eval:[ 17/225] data_time 0.039881 (0.067765) train_time 0.798075 (0.810749)
#Eval:[ 18/225] data_time 0.040542 (0.066332) train_time 0.802576 (0.810319)
#Eval:[ 19/225] data_time 0.039582 (0.064995) train_time 0.788466 (0.809226)
#Eval:[ 20/225] data_time 0.040563 (0.063831) train_time 0.796365 (0.808614)
#Eval:[ 21/225] data_time 0.040506 (0.062771) train_time 0.795652 (0.808025)
#Eval:[ 22/225] data_time 0.040458 (0.061801) train_time 0.797857 (0.807582)
#Eval:[ 23/225] data_time 0.040882 (0.060929) train_time 0.797897 (0.807179)
#Eval:[ 24/225] data_time 0.040913 (0.060129) train_time 0.798708 (0.806840)
#Eval:[ 25/225] data_time 0.040960 (0.059391) train_time 0.803163 (0.806699)
#Eval:[ 26/225] data_time 0.040093 (0.058677) train_time 0.799866 (0.806446)
#Eval:[ 27/225] data_time 0.039694 (0.057999) train_time 0.797520 (0.806127)
#Eval:[ 28/225] data_time 0.039761 (0.057370) train_time 0.800132 (0.805920)
#Eval:[ 29/225] data_time 0.040533 (0.056809) train_time 0.799073 (0.805692)
#Eval:[ 30/225] data_time 0.040257 (0.056275) train_time 0.806425 (0.805716)
#Eval:[ 31/225] data_time 0.039992 (0.055766) train_time 0.801387 (0.805580)
#Eval:[ 32/225] data_time 0.040647 (0.055308) train_time 0.805682 (0.805583)
#Eval:[ 33/225] data_time 0.040515 (0.054873) train_time 0.801444 (0.805462)
#Eval:[ 34/225] data_time 0.041032 (0.054477) train_time 0.811721 (0.805640)
#Eval:[ 35/225] data_time 0.040896 (0.054100) train_time 0.803612 (0.805584)
#Eval:[ 36/225] data_time 0.040744 (0.053739) train_time 0.809601 (0.805693)
#Eval:[ 37/225] data_time 0.041418 (0.053415) train_time 0.805974 (0.805700)
#Eval:[ 38/225] data_time 0.040259 (0.053077) train_time 0.810290 (0.805818)
#Eval:[ 39/225] data_time 0.041094 (0.052778) train_time 0.803531 (0.805761)
#Eval:[ 40/225] data_time 0.039910 (0.052464) train_time 0.807249 (0.805797)
#Eval:[ 41/225] data_time 0.040536 (0.052180) train_time 0.806144 (0.805805)
#Eval:[ 42/225] data_time 0.042400 (0.051952) train_time 0.807435 (0.805843)
#Eval:[ 43/225] data_time 0.043432 (0.051759) train_time 0.811019 (0.805961)
#Eval:[ 44/225] data_time 0.041226 (0.051525) train_time 0.807243 (0.805989)
#Eval:[ 45/225] data_time 0.040811 (0.051292) train_time 0.810134 (0.806079)
#Eval:[ 46/225] data_time 0.041412 (0.051082) train_time 0.809040 (0.806142)
#Eval:[ 47/225] data_time 0.041421 (0.050880) train_time 0.811074 (0.806245)
#Eval:[ 48/225] data_time 0.040816 (0.050675) train_time 0.808080 (0.806282)
#Eval:[ 49/225] data_time 0.041842 (0.050498) train_time 0.819847 (0.806554)
#Eval:[ 50/225] data_time 0.040665 (0.050306) train_time 0.804493 (0.806513)
#Eval:[ 51/225] data_time 0.040511 (0.050117) train_time 0.817381 (0.806722)
#Eval:[ 52/225] data_time 0.044540 (0.050012) train_time 0.810324 (0.806790)
#Eval:[ 53/225] data_time 0.040196 (0.049830) train_time 0.811689 (0.806881)
#Eval:[ 54/225] data_time 0.040613 (0.049663) train_time 0.807991 (0.806901)
#Eval:[ 55/225] data_time 0.041492 (0.049517) train_time 0.812014 (0.806993)
#Eval:[ 56/225] data_time 0.039906 (0.049348) train_time 0.803624 (0.806933)
#Eval:[ 57/225] data_time 0.044075 (0.049257) train_time 0.814005 (0.807055)
#Eval:[ 58/225] data_time 0.040814 (0.049114) train_time 0.805577 (0.807030)
#Eval:[ 59/225] data_time 0.040640 (0.048973) train_time 0.808917 (0.807062)
#Eval:[ 60/225] data_time 0.040619 (0.048836) train_time 0.807464 (0.807068)
#Eval:[ 61/225] data_time 0.042691 (0.048737) train_time 0.813154 (0.807166)
#Eval:[ 62/225] data_time 0.040645 (0.048608) train_time 0.814715 (0.807286)
#Eval:[ 63/225] data_time 0.040831 (0.048487) train_time 0.811918 (0.807359)
#Eval:[ 64/225] data_time 0.040498 (0.048364) train_time 0.811884 (0.807428)
#Eval:[ 65/225] data_time 0.039673 (0.048232) train_time 0.814446 (0.807535)
#Eval:[ 66/225] data_time 0.040010 (0.048110) train_time 0.816979 (0.807676)
#Eval:[ 67/225] data_time 0.040763 (0.048001) train_time 0.815673 (0.807793)
#Eval:[ 68/225] data_time 0.040116 (0.047887) train_time 0.815871 (0.807910)
#Eval:[ 69/225] data_time 0.040113 (0.047776) train_time 0.812022 (0.807969)
#Eval:[ 70/225] data_time 0.042265 (0.047699) train_time 0.819192 (0.808127)
#Eval:[ 71/225] data_time 0.040488 (0.047598) train_time 0.802501 (0.808049)
#Eval:[ 72/225] data_time 0.041070 (0.047509) train_time 0.805149 (0.808009)
#Eval:[ 73/225] data_time 0.042054 (0.047435) train_time 0.815068 (0.808105)
#Eval:[ 74/225] data_time 0.040750 (0.047346) train_time 0.809044 (0.808117)
#Eval:[ 75/225] data_time 0.040011 (0.047250) train_time 0.813235 (0.808184)
#Eval:[ 76/225] data_time 0.043043 (0.047195) train_time 0.811157 (0.808223)
#Eval:[ 77/225] data_time 0.039876 (0.047101) train_time 0.813111 (0.808286)
#Eval:[ 78/225] data_time 0.040135 (0.047013) train_time 0.810924 (0.808319)
#Eval:[ 79/225] data_time 0.040306 (0.046929) train_time 0.812062 (0.808366)
#Eval:[ 80/225] data_time 0.040752 (0.046853) train_time 0.809658 (0.808382)
#Eval:[ 81/225] data_time 0.040653 (0.046777) train_time 0.816320 (0.808479)
#Eval:[ 82/225] data_time 0.040388 (0.046700) train_time 0.810328 (0.808501)
#Eval:[ 83/225] data_time 0.040740 (0.046629) train_time 0.816155 (0.808592)
#Eval:[ 84/225] data_time 0.041280 (0.046566) train_time 0.813080 (0.808645)
#Eval:[ 85/225] data_time 0.040848 (0.046500) train_time 0.813959 (0.808707)
#Eval:[ 86/225] data_time 0.040094 (0.046426) train_time 0.814204 (0.808770)
#Eval:[ 87/225] data_time 0.040827 (0.046363) train_time 0.809299 (0.808776)
#Eval:[ 88/225] data_time 0.039530 (0.046286) train_time 0.811571 (0.808807)
#Eval:[ 89/225] data_time 0.040482 (0.046221) train_time 0.806065 (0.808777)
#Eval:[ 90/225] data_time 0.040568 (0.046159) train_time 0.813799 (0.808832)
#Eval:[ 91/225] data_time 0.041428 (0.046108) train_time 0.812696 (0.808874)
#Eval:[ 92/225] data_time 0.040262 (0.046045) train_time 0.807937 (0.808864)
#Eval:[ 93/225] data_time 0.041116 (0.045993) train_time 0.808364 (0.808859)
#Eval:[ 94/225] data_time 0.040158 (0.045931) train_time 0.811798 (0.808890)
#Eval:[ 95/225] data_time 0.040652 (0.045876) train_time 0.807996 (0.808880)
#Eval:[ 96/225] data_time 0.040504 (0.045821) train_time 0.819683 (0.808992)
#Eval:[ 97/225] data_time 0.040604 (0.045767) train_time 0.810562 (0.809008)
#Eval:[ 98/225] data_time 0.040298 (0.045712) train_time 0.818260 (0.809101)
#Eval:[ 99/225] data_time 0.040197 (0.045657) train_time 0.813555 (0.809146)
#Eval:[100/225] data_time 0.042036 (0.045621) train_time 0.820814 (0.809261)
#Eval:[101/225] data_time 0.042076 (0.045586) train_time 0.820296 (0.809369)
#Eval:[102/225] data_time 0.042270 (0.045554) train_time 0.819977 (0.809472)
#Eval:[103/225] data_time 0.040020 (0.045501) train_time 0.821351 (0.809587)
#Eval:[104/225] data_time 0.040334 (0.045452) train_time 0.814307 (0.809631)
#Eval:[105/225] data_time 0.041071 (0.045411) train_time 0.819901 (0.809728)
#Eval:[106/225] data_time 0.040657 (0.045366) train_time 0.816109 (0.809788)
#Eval:[107/225] data_time 0.041048 (0.045326) train_time 0.819442 (0.809877)
#Eval:[108/225] data_time 0.041171 (0.045288) train_time 0.816974 (0.809942)
#Eval:[109/225] data_time 0.040030 (0.045240) train_time 0.816332 (0.810001)
#Eval:[110/225] data_time 0.040808 (0.045200) train_time 0.812515 (0.810023)
#Eval:[111/225] data_time 0.040519 (0.045158) train_time 0.816895 (0.810085)
#Eval:[112/225] data_time 0.041322 (0.045125) train_time 0.816286 (0.810139)
#Eval:[113/225] data_time 0.040582 (0.045085) train_time 0.814588 (0.810178)
#Eval:[114/225] data_time 0.042142 (0.045059) train_time 0.820069 (0.810264)
#Eval:[115/225] data_time 0.041483 (0.045028) train_time 0.814595 (0.810302)
#Eval:[116/225] data_time 0.041713 (0.045000) train_time 0.820677 (0.810390)
#Eval:[117/225] data_time 0.041497 (0.044970) train_time 0.815148 (0.810431)
#Eval:[118/225] data_time 0.039872 (0.044927) train_time 0.818884 (0.810502)
#Eval:[119/225] data_time 0.040807 (0.044893) train_time 0.814259 (0.810533)
#Eval:[120/225] data_time 0.042302 (0.044872) train_time 0.820152 (0.810613)
#Eval:[121/225] data_time 0.040751 (0.044838) train_time 0.815587 (0.810653)
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#Eval:[125/225] data_time 0.040888 (0.044709) train_time 0.819381 (0.810940)
#Eval:[126/225] data_time 0.041299 (0.044682) train_time 0.818301 (0.810998)
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#Eval:[128/225] data_time 0.040050 (0.044626) train_time 0.819672 (0.811150)
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extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.010062171146273613
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:25 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.9992985725402832
dmean : 0.00032108312007039785
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.009366649203002453
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:31 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.9998121857643127
dmean : 0.0003922517935279757
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.011957003735005856
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:37 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.9996381998062134
dmean : 0.014132329262793064
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09444835036993027
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:43 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.999423623085022
dmean : 0.0008302876376546919
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.021966466680169106
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:49 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling created
Origin: [0.0, 0.0, 0.0]
detected mode mapc 1, mapr 2, maps 3
information of /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/input.mrc
The recording mode in the mrc file:2
XYZ dim:271,271,271
location of first column/row/section in unit cell:0,0,0
sampling along X,Y,Z axis of unit cell:271,271,271
cell dimensions in angstroms:271.000000,271.000000,271.000000
Cell angles in degree:90,90,90
axis mode:(1,2,3)
density statistics:min(-2.006058),max(3.159605),mean(0.012243)
space group number:1
extended data:0
origin state:(0.000000,0.000000,0.000000)
density data shape:
(271, 271, 271)
min density:0.000000
max density:3.159605
number of voxels: 19902511
width of x,y,z:(1.000000,1.000000,1.000000)
order mode:1
useful points: 16288
in total chain useful percentage 0.000818
after normalizing pho dens min 0.0000 max 0.9997
useful points: 22051
in total chain useful percentage 0.001108
dens shape now
(271, 271, 271)
after normalizing sugar dens min 0.0000 max 0.9996
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/pho_LDP created
carry on mean shifting jobs
useful points 16288
set up filters
fmaxd=6.000000
mean shift 0 / 16288
mean shift 1000 / 16288
mean shift 2000 / 16288
mean shift 3000 / 16288
mean shift 4000 / 16288
mean shift 5000 / 16288
mean shift 6000 / 16288
mean shift 7000 / 16288
mean shift 8000 / 16288
mean shift 9000 / 16288
mean shift 10000 / 16288
mean shift 11000 / 16288
mean shift 12000 / 16288
mean shift 13000 / 16288
mean shift 14000 / 16288
mean shift 15000 / 16288
mean shift 16000 / 16288
finishing meanshifting with 16288 points
here we get the density range 9.485158
0
10000
merging finishing with 141 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.600675582885742
dmean : 5.57807506993413e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.021728407591581345
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:07:24 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 34 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_LDP created
carry on mean shifting jobs
useful points 22051
set up filters
fmaxd=6.000000
mean shift 0 / 22051
mean shift 1000 / 22051
mean shift 2000 / 22051
mean shift 3000 / 22051
mean shift 4000 / 22051
mean shift 5000 / 22051
mean shift 6000 / 22051
mean shift 7000 / 22051
mean shift 8000 / 22051
mean shift 9000 / 22051
mean shift 10000 / 22051
mean shift 11000 / 22051
mean shift 12000 / 22051
mean shift 13000 / 22051
mean shift 14000 / 22051
mean shift 15000 / 22051
mean shift 16000 / 22051
mean shift 17000 / 22051
mean shift 18000 / 22051
mean shift 19000 / 22051
mean shift 20000 / 22051
mean shift 21000 / 22051
mean shift 22000 / 22051
finishing meanshifting with 22051 points
here we get the density range 9.946610
0
10000
20000
merging finishing with 181 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.048613548278809
dmean : 7.974963955348358e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.027282539755105972
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:07:47 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 57 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_graph created
0
10000
20000
number of possible connected edges by differen ori data:313
skip edges with distance 14.777493
skip edges with distance 15.687752
skip edges with distance 13.441810
skip edges with distance 12.313532
skip edges with distance 11.735175
skip edges with distance 10.331086
skip edges with distance 10.178144
skip edges with distance 10.254010
skip edges with distance 11.361568
skip edges with distance 10.557541
skip edges with distance 10.159017
skip edges with distance 18.316433
skip edges with distance 14.009447
skip edges with distance 10.096806
skip edges with distance 11.412779
skip edges with distance 11.492459
skip edges with distance 11.367592
skip edges with distance 12.261071
skip edges with distance 10.064836
skip edges with distance 11.036328
skip edges with distance 11.381088
skip edges with distance 15.269321
sorting edge for MST preparataion 288
filtered edge numbers 313
297/313 edges are remained after prob map checking
filtered edge numbers 297
Further adding 240 edges based on extending and checking base region
filtered edge numbers 537
0
edge density min 1.00 max 200.78 mean 14.83
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search/sub_graph0 created
filtered edge numbers 537
number of edges in the data: 1025
distance mean 1548.454634
updated distance mean 46744.975788
number vehicles: 5 adj matrix shape: 182
drop penalty 42156
start routing
add capacity
add penalty
add params
Objective: 213867
Route for vehicle 0:
0 -> 15 -> 20 -> 12 -> 13 -> 8 -> 1 -> 10 -> 14 -> 22 -> 23 -> 25 -> 27 -> 32 -> 30 -> 28 -> 34 -> 37 -> 35 -> 38 -> 42 -> 41 -> 48 -> 47 -> 46 -> 54 -> 52 -> 55 -> 58 -> 57 -> 66 -> 63 -> 61 -> 62 -> 67 -> 71 -> 68 -> 72 -> 73 -> 74 -> 75 -> 78 -> 84 -> 83 -> 93 -> 91 -> 92 -> 97 -> 96 -> 102 -> 101 -> 106 -> 104 -> 110 -> 107 -> 109 -> 113 -> 114 -> 115 -> 116 -> 119 -> 122 -> 117 -> 118 -> 123 -> 124 -> 129 -> 132 -> 131 -> 143 -> 137 -> 138 -> 146 -> 148 -> 155 -> 152 -> 159 -> 162 -> 156 -> 166 -> 157 -> 158 -> 161 -> 163 -> 165 -> 164 -> 169 -> 171 -> 174 -> 172 -> 176 -> 181 -> 178 -> 180 -> 179 -> 177 -> 173 -> 175 -> 170 -> 167 -> 154 -> 153 -> 150 -> 151 -> 149 -> 147 -> 145 -> 144 -> 140 -> 136 -> 139 -> 135 -> 141 -> 142 -> 133 -> 134 -> 130 -> 127 -> 125 -> 126 -> 120 -> 121 -> 112 -> 111 -> 108 -> 105 -> 103 -> 99 -> 98 -> 100 -> 95 -> 94 -> 89 -> 88 -> 90 -> 85 -> 86 -> 87 -> 81 -> 82 -> 80 -> 77 -> 79 -> 76 -> 70 -> 69 -> 65 -> 60 -> 56 -> 53 -> 51 -> 50 -> 49 -> 44 -> 45 -> 43 -> 40 -> 39 -> 36 -> 33 -> 31 -> 29 -> 21 -> 24 -> 19 -> 18 -> 17 -> 11 -> 9 -> 3 -> 2 -> 7 -> 5 -> 6 -> 4 -> 0
Distance of the route: 165891m
Route for vehicle 1:
0 -> 64 -> 59 -> 0
Distance of the route: 20675m
Route for vehicle 2:
0 -> 128 -> 0
Distance of the route: 0m
Route for vehicle 3:
0 -> 26 -> 16 -> 0
Distance of the route: 20698m
Route for vehicle 4:
0 -> 160 -> 168 -> 0
Distance of the route: 6603m
Maximum of the route distances: 165891m
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search/sub_graph0/Prune created
Extract search dict 174, GT search dict 181
search length 174, return search result length 174
filtered edge numbers 536
174 node path find 1 sub path
in total we collected 1 path candidates
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_LDP created
useful points: 2709
in total chain useful percentage 0.000136
after normalizing pho dens min 0.0000 max 0.9988
carry on mean shifting jobs
useful points 2709
set up filters
fmaxd=6.000000
mean shift 0 / 2709
mean shift 1000 / 2709
mean shift 2000 / 2709
finishing meanshifting with 2709 points
here we get the density range 9.808118
0
merging finishing with 33 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.931495666503906
dmean : 1.1405014447518624e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.009559660218656063
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:22 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 9 isolated grid points
useful points: 3178
in total chain useful percentage 0.000160
after normalizing pho dens min 0.0000 max 0.9996
carry on mean shifting jobs
useful points 3178
set up filters
fmaxd=6.000000
mean shift 0 / 3178
mean shift 1000 / 3178
mean shift 2000 / 3178
mean shift 3000 / 3178
finishing meanshifting with 3178 points
here we get the density range 9.771262
0
merging finishing with 33 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.886703491210938
dmean : 1.1659149095066823e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.009832863695919514
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:29 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 13 isolated grid points
useful points: 2960
in total chain useful percentage 0.000149
after normalizing pho dens min 0.0000 max 0.9993
carry on mean shifting jobs
useful points 2960
set up filters
fmaxd=6.000000
mean shift 0 / 2960
mean shift 1000 / 2960
mean shift 2000 / 2960
finishing meanshifting with 2960 points
here we get the density range 9.877241
0
merging finishing with 34 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.980541229248047
dmean : 8.555003660148941e-06
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.00806853361427784
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:37 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 56 isolated grid points
useful points: 5616
in total chain useful percentage 0.000282
after normalizing pho dens min 0.0000 max 0.9998
carry on mean shifting jobs
useful points 5616
set up filters
fmaxd=6.000000
mean shift 0 / 5616
mean shift 1000 / 5616
mean shift 2000 / 5616
mean shift 3000 / 5616
mean shift 4000 / 5616
mean shift 5000 / 5616
finishing meanshifting with 5616 points
here we get the density range 9.979040
0
merging finishing with 52 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.098882675170898
dmean : 1.816607800719794e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.012404625304043293
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:46 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 27 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_LDP existed
useful points: 13816
in total chain useful percentage 0.000694
after normalizing pho dens min 0.0000 max 0.9994
carry on mean shifting jobs
useful points 13816
set up filters
fmaxd=6.000000
mean shift 0 / 13816
mean shift 1000 / 13816
mean shift 2000 / 13816
mean shift 3000 / 13816
mean shift 4000 / 13816
mean shift 5000 / 13816
mean shift 6000 / 13816
mean shift 7000 / 13816
mean shift 8000 / 13816
mean shift 9000 / 13816
mean shift 10000 / 13816
mean shift 11000 / 13816
mean shift 12000 / 13816
mean shift 13000 / 13816
finishing meanshifting with 13816 points
here we get the density range 6.504001
0
10000
merging finishing with 116 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
Starting phenix.real_space_refine (version: 1.20)
on Fri Jun 9 14:19:52 2023 by webdklab
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb
Found real_map, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
resolution=3.7000
output.suffix=_phenix_refine
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
default_real_map = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
model {
file = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb"
}
default_model = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb"
}
resolution = 3.7000
output {
suffix = _phenix_refine
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.038
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.00s
Monomer Library directory:
"/apps/phenix/phenix-1.20-4459/modules/chem_data/mon_lib"
Total number of atoms: 2132
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2132
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 97, 2132
Inner-chain residues flagged as termini: ['pdbres=" G A 2 "', 'pdbres=" G A 3 "', 'pdbres=" U A 4 "', 'pdbres=" U A 5 "', 'pdbres=" U A 6 "', 'pdbres=" G A 7 "', 'pdbres=" G A 8 "', 'pdbres=" G A 9 "', 'pdbres=" A A 10 "', 'pdbres=" U A 11 "', 'pdbres=" A A 12 "', 'pdbres=" C A 13 "', 'pdbres=" C A 14 "', 'pdbres=" U A 15 "', 'pdbres=" G A 16 "', 'pdbres=" U A 17 "', 'pdbres=" U A 18 "', 'pdbres=" C A 19 "', 'pdbres=" C A 20 "', 'pdbres=" C A 21 "', 'pdbres=" C A 22 "', 'pdbres=" C A 23 "', 'pdbres=" U A 24 "', 'pdbres=" U A 25 "', 'pdbres=" U A 26 "', 'pdbres=" A A 27 "', 'pdbres=" C A 28 "', 'pdbres=" A A 29 "', 'pdbres=" A A 30 "', 'pdbres=" G A 31 "', 'pdbres=" C A 32 "', 'pdbres=" C A 33 "', 'pdbres=" A A 34 "', 'pdbres=" C A 35 "', 'pdbres=" G A 36 "', 'pdbres=" G A 37 "', 'pdbres=" G A 38 "', 'pdbres=" U A 39 "', 'pdbres=" U A 40 "', 'pdbres=" A A 41 "', 'pdbres=" U A 42 "', 'pdbres=" U A 43 "', 'pdbres=" G A 44 "', 'pdbres=" U A 45 "', 'pdbres=" U A 46 "', 'pdbres=" G A 47 "', 'pdbres=" G A 48 "', 'pdbres=" G A 49 "', 'pdbres=" U A 50 "', 'pdbres=" U A 51 "', 'pdbres=" G A 52 "', 'pdbres=" C A 53 "', 'pdbres=" C A 54 "', 'pdbres=" C A 55 "', 'pdbres=" C A 56 "', 'pdbres=" C A 57 "', 'pdbres=" C A 58 "', 'pdbres=" C A 59 "', 'pdbres=" C A 60 "', 'pdbres=" C A 61 "', 'pdbres=" A A 62 "', 'pdbres=" U A 63 "', 'pdbres=" C A 64 "', 'pdbres=" U A 65 "', 'pdbres=" U A 66 "', 'pdbres=" U A 67 "', 'pdbres=" A A 68 "', 'pdbres=" C A 69 "', 'pdbres=" U A 70 "', 'pdbres=" U A 71 "', 'pdbres=" G A 72 "', 'pdbres=" G A 73 "', 'pdbres=" C A 74 "', 'pdbres=" U A 75 "', 'pdbres=" C A 76 "', 'pdbres=" C A 77 "', 'pdbres=" C A 78 "', 'pdbres=" U A 79 "', 'pdbres=" U A 80 "', 'pdbres=" A A 81 "', 'pdbres=" A A 82 "', 'pdbres=" G A 83 "', 'pdbres=" U A 84 "', 'pdbres=" G A 85 "', 'pdbres=" U A 86 "', 'pdbres=" U A 87 "', 'pdbres=" A A 88 "', 'pdbres=" C A 89 "', 'pdbres=" A A 90 "', 'pdbres=" G A 91 "', 'pdbres=" G A 92 "', 'pdbres=" G A 93 "', 'pdbres=" C A 94 "', 'pdbres=" C A 95 "', 'pdbres=" U A 96 "']
Classifications: {'RNA': 97}
Modifications used: {'rna2p_pur': 36, 'p5*END': 97, 'rna2p_pyr': 61}
Link IDs: {'rna2p': 96}
Chain breaks: 20
Time building chain proxies: 0.62, per 1000 atoms: 0.29
Number of scatterers: 2132
At special positions: 0
Unit cell: (49, 59, 138, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
P 97 15.00
O 794 8.00
N 332 7.00
C 909 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.98
Conformation dependent library (CDL) restraints added in 5.4 milliseconds
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 0
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 0 sheets defined
0.0% alpha, 0.0% beta
11 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.24
Creating SS restraints...
No hydrogen bonds defined for protein.
Restraints generated for nucleic acids:
22 hydrogen bonds
20 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 0.16
Time building geometry restraints manager: 0.80 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.25 - 0.80: 40
0.80 - 1.34: 325
1.34 - 1.89: 1955
1.89 - 2.44: 9
2.44 - 2.98: 12
Warning: very small bond lengths.
Bond restraints: 2341
Sorted by residual:
bond pdb="O3' C A 61 "
pdb="P A A 62 "
ideal model delta sigma weight residual
1.607 2.984 -1.377 1.50e-02 4.44e+03 8.43e+03
bond pdb="O3' A A 62 "
pdb="P U A 63 "
ideal model delta sigma weight residual
1.607 2.978 -1.371 1.50e-02 4.44e+03 8.35e+03
bond pdb="O3' G A 8 "
pdb="P G A 9 "
ideal model delta sigma weight residual
1.607 0.249 1.358 1.50e-02 4.44e+03 8.20e+03
bond pdb="O3' G A 16 "
pdb="P U A 17 "
ideal model delta sigma weight residual
1.607 2.958 -1.351 1.50e-02 4.44e+03 8.12e+03
bond pdb="O3' A A 30 "
pdb="P G A 31 "
ideal model delta sigma weight residual
1.607 0.256 1.351 1.50e-02 4.44e+03 8.11e+03
... (remaining 2336 not shown)
Histogram of bond angle deviations from ideal:
2.96 - 33.68: 30
33.68 - 64.39: 63
64.39 - 95.11: 96
95.11 - 125.82: 3368
125.82 - 156.53: 174
Bond angle restraints: 3731
Sorted by residual:
angle pdb="C3' C A 23 "
pdb="O3' C A 23 "
pdb="P U A 24 "
ideal model delta sigma weight residual
120.20 15.25 104.95 1.50e+00 4.44e-01 4.90e+03
angle pdb="C3' U A 17 "
pdb="O3' U A 17 "
pdb="P U A 18 "
ideal model delta sigma weight residual
120.20 15.49 104.71 1.50e+00 4.44e-01 4.87e+03
angle pdb="C3' C A 33 "
pdb="O3' C A 33 "
pdb="P A A 34 "
ideal model delta sigma weight residual
120.20 16.30 103.90 1.50e+00 4.44e-01 4.80e+03
angle pdb="C3' C A 89 "
pdb="O3' C A 89 "
pdb="P A A 90 "
ideal model delta sigma weight residual
120.20 18.72 101.48 1.50e+00 4.44e-01 4.58e+03
angle pdb="C3' U A 26 "
pdb="O3' U A 26 "
pdb="P A A 27 "
ideal model delta sigma weight residual
120.20 19.91 100.29 1.50e+00 4.44e-01 4.47e+03
... (remaining 3726 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 32.33: 423
32.33 - 64.66: 447
64.66 - 96.98: 101
96.98 - 129.31: 101
129.31 - 161.64: 29
Dihedral angle restraints: 1101
sinusoidal: 1101
harmonic: 0
Sorted by residual:
dihedral pdb="C5' G A 49 "
pdb="C4' G A 49 "
pdb="C3' G A 49 "
pdb="O3' G A 49 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.20 -114.80 1 8.00e+00 1.56e-02 2.13e+02
dihedral pdb="C5' G A 38 "
pdb="C4' G A 38 "
pdb="C3' G A 38 "
pdb="O3' G A 38 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.20 -114.80 1 8.00e+00 1.56e-02 2.13e+02
dihedral pdb="C5' G A 16 "
pdb="C4' G A 16 "
pdb="C3' G A 16 "
pdb="O3' G A 16 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.21 -114.79 1 8.00e+00 1.56e-02 2.13e+02
... (remaining 1098 not shown)
Histogram of chiral volume deviations from ideal:
0.533 - 1.519: 97
1.519 - 2.506: 0
2.506 - 3.493: 0
3.493 - 4.480: 0
4.480 - 5.466: 388
Chirality restraints: 485
Sorted by residual:
chirality pdb="C3' G A 9 "
pdb="C4' G A 9 "
pdb="O3' G A 9 "
pdb="C2' G A 9 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
chirality pdb="C3' C A 64 "
pdb="C4' C A 64 "
pdb="O3' C A 64 "
pdb="C2' C A 64 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
chirality pdb="C3' C A 20 "
pdb="C4' C A 20 "
pdb="O3' C A 20 "
pdb="C2' C A 20 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
... (remaining 482 not shown)
Planarity restraints: 97
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb="C1' G A 73 " -0.000 2.00e-02 2.50e+03 1.93e-03 1.11e-01
pdb="N9 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="C8 G A 73 " -0.001 2.00e-02 2.50e+03
pdb="N7 G A 73 " 0.000 2.00e-02 2.50e+03
pdb="C5 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="C6 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="O6 G A 73 " 0.002 2.00e-02 2.50e+03
pdb="N1 G A 73 " -0.006 2.00e-02 2.50e+03
pdb="C2 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="N2 G A 73 " 0.002 2.00e-02 2.50e+03
pdb="N3 G A 73 " 0.000 2.00e-02 2.50e+03
pdb="C4 G A 73 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' G A 83 " 0.000 2.00e-02 2.50e+03 1.92e-03 1.11e-01
pdb="N9 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C8 G A 83 " 0.000 2.00e-02 2.50e+03
pdb="N7 G A 83 " 0.001 2.00e-02 2.50e+03
pdb="C5 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C6 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="O6 G A 83 " -0.002 2.00e-02 2.50e+03
pdb="N1 G A 83 " 0.006 2.00e-02 2.50e+03
pdb="C2 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="N2 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="N3 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C4 G A 83 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' G A 3 " -0.000 2.00e-02 2.50e+03 1.90e-03 1.09e-01
pdb="N9 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C8 G A 3 " -0.001 2.00e-02 2.50e+03
pdb="N7 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C5 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C6 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="O6 G A 3 " 0.002 2.00e-02 2.50e+03
pdb="N1 G A 3 " -0.006 2.00e-02 2.50e+03
pdb="C2 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="N2 G A 3 " 0.002 2.00e-02 2.50e+03
pdb="N3 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C4 G A 3 " -0.000 2.00e-02 2.50e+03
... (remaining 94 not shown)
Histogram of nonbonded interaction distances:
0.15 - 1.10: 253
1.10 - 2.05: 1451
2.05 - 3.00: 4387
3.00 - 3.95: 8441
3.95 - 4.90: 11326
Warning: very small nonbonded interaction distances.
Nonbonded interactions: 25858
Sorted by model distance:
nonbonded pdb="O2 U A 11 "
pdb="C4' A A 12 "
model vdw
0.149 3.470
nonbonded pdb="O2' U A 96 "
pdb="OP2 C A 97 "
model vdw
0.243 2.440
nonbonded pdb="O2' C A 54 "
pdb="C1' C A 55 "
model vdw
0.316 3.470
nonbonded pdb="P G A 3 "
pdb="O3' G A 7 "
model vdw
0.322 3.400
nonbonded pdb="O2' A A 10 "
pdb="OP1 U A 11 "
model vdw
0.334 2.440
... (remaining 25853 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
P 97 5.49 5
C 909 2.51 5
N 332 2.21 5
O 794 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 5
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Write .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.530
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 1.020
Check model and map are aligned: 0.000
Convert atoms to be neutral: 0.050
Process input model: 3.850
Find NCS groups from input model: 0.010
Set up NCS constraints: 0.000
Set refine NCS operators: 0.000
Set scattering table: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:0.810
Set ADP refinement strategy: 0.000
Write .geo file: 1.260
Internal consistency checks: 0.000
Total: 7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2593
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.186 1.377 2341 Z=11.123
Angle : 13.450 105.036 3731 Z= 7.571
Chirality : 4.688 5.466 485
Planarity : 0.002 0.002 97
Dihedral : 58.071 161.640 1101
Min Nonbonded Distance : 0.149
Molprobity Statistics.
All-atom Clashscore : 206.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0185
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0068
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.9980
chunk 2 optimal weight: 0.9980
chunk 3 optimal weight: 0.9990
chunk 4 optimal weight: 0.9980
chunk 5 optimal weight: 1.9990
chunk 6 optimal weight: 0.8980
chunk 7 optimal weight: 0.7980
chunk 8 optimal weight: 0.6980
overall best weight: 0.8480
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2712
moved from start: 1.9161
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.037 0.623 2341 Z= 1.897
Angle : 6.445 65.919 3731 Z= 2.425
Chirality : 0.394 3.773 485
Planarity : 0.014 0.050 97
Dihedral : 42.046 176.109 1101
Min Nonbonded Distance : 1.664
Molprobity Statistics.
All-atom Clashscore : 78.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.025
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0288
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.019
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0072
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 5.9990
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 0.9980
chunk 3 optimal weight: 0.5980
chunk 4 optimal weight: 2.9990
chunk 5 optimal weight: 4.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.0483
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3790
moved from start: 2.4979
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.603 2341 Z= 1.810
Angle : 5.835 51.003 3731 Z= 2.141
Chirality : 0.375 3.699 485
Planarity : 0.009 0.042 97
Dihedral : 35.827 178.320 1101
Min Nonbonded Distance : 1.673
Molprobity Statistics.
All-atom Clashscore : 70.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.025
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0199
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0067
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 1.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 7.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 0.9980
overall best weight: 1.4988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4681
moved from start: 2.6838
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.600 2341 Z= 1.796
Angle : 5.803 50.069 3731 Z= 2.104
Chirality : 0.345 3.697 485
Planarity : 0.008 0.040 97
Dihedral : 34.571 163.364 1101
Min Nonbonded Distance : 1.674
Molprobity Statistics.
All-atom Clashscore : 81.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.036
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0288
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.017
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 7.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7490
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5132
moved from start: 2.9035
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.602 2341 Z= 1.806
Angle : 5.795 50.423 3731 Z= 2.094
Chirality : 0.345 3.699 485
Planarity : 0.008 0.042 97
Dihedral : 34.334 169.496 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 92.40
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.015
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0190
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0068
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.8980
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 9.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.116062 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.105365 restraints weight = 14392.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.106936 restraints weight = 6649.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.107952 restraints weight = 4363.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start: 2.9877
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.598 2341 Z= 1.796
Angle : 5.766 50.227 3731 Z= 2.078
Chirality : 0.347 3.682 485
Planarity : 0.008 0.042 97
Dihedral : 34.038 179.879 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 87.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
===============================================================================
Job complete
usr+sys time: 189.89 seconds
wall clock time: 5 minutes 22.26 seconds (322.26 seconds total)
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /apps/ccp4/ccp4-8.0/lib/data/monomers/
There are 249 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ALA.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ASP.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ASN.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/CYS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLN.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLY.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLU.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PHE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/h/HIS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/i/ILE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/l/LYS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/l/LEU.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/m/MET.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/m/MSE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PRO.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ARG.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/s/SER.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/THR.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/v/VAL.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/TRP.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/TYR.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PO4.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/s/SO4.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GOL.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/CIT.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/e/EDO.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/A.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/C.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/G.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/u/U.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DA.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DC.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DG.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DT.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/h/HOH.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/n/NA.cif
Spacegroup: P 1
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
INFO:: coot.py imported
Running python script /net/apps-server/ccp4/ccp4-8.0/coot_py2/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Kihara, Welcome to Coot version 0.9.8.7
[1m(set-display-intro-string "Good Afternoon Kihara, Welcome to Coot version 0.9.8.7")[0m
[1m(use-graphics-interface-state)[0m
INFO:: preferences directory /bio/dragon/webdklab/.coot-preferences does not exist. Won't read preferences.
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
Good afternoon Kihara Lab Web User,UMS. Welcome to Coot 0.9.8.7.
[1m(set-display-intro-string "Good afternoon Kihara. Welcome to Coot 0.9.8.7")[0m
[1m(set-display-lists-for-maps 1)[0m
INFO:: preferences directory /bio/dragon/webdklab/.coot-preferences does not exist. Won't read .scm preferences.
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
INFO:: There are 1 command line scripts to run
coot_refine.py
calling run_script() for file coot_refine.py
debug:: run_script() on coot_refine.py
Running python script coot_refine.py
[1m(handle-read-draw-molecule-with-recentre "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb" 1)[0m
INFO:: Reading coordinate file: /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb
INFO:: file /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
debug:: g.safe_scheme_command() with command post-read-model-hook
INFO:: in run_post_read_model_hook() pFunc 0xed2b40 is not callable
INFO:: in run_post_read_model_hook() pDict 0x7f92bd155168
INFO:: in run_post_read_model_hook() pModule 0x7f92bd141be8
Molecule 0 read successfully
INFO:: map file type was determined to be CCP4 type
DEBUG:: init xmap with P 1 Cell ( 271, 271, 271, 90, 90, 90) Nuvw = ( 271, 271, 271)
INFO:: map read 519 milliseconds
0.0789901 19871549 ****************************************************************************************************|
0.23697 542
0.394951 6095
0.552931 5823
0.710911 4535
0.868891 3427
1.02687 2888
1.18485 2311
1.34283 1788
1.50081 1260
1.65879 854
1.81677 571
1.97475 378
2.13273 215
2.29071 122
2.44869 90
2.60667 40
2.76465 11
2.92263 7
3.08062 4
3.2386 1
Pre-filter Map statistics: mean: 0.00131928 st.d: 0.0376485
Pre-filter Map statistics: min: 0 max: 3.15961
INFO:: n grid points: 19902511
INFO:: mean before filtering: 0.00131928
INFO:: variance before filtering: 0.00141741
INFO:: filter by ignoring 19871549 of 19902511 counts ( = 99.84%) with values around 0.000158 bounds 0 0.000316 from bin-number 0 of 10000
Post-filter Map statistics: mean: 0.848 st.d: 0.4394
Post-filter Map statistics: min: 0 max: 3.16
INFO:: map_density_distribution() took 179 milliseconds
------------------------- em 1 contour_level 1.977
Map extents: ..... 271 271 271
Map mean: ........ 0.848
Map rmsd: ........ 0.4394
Map maximum: ..... 3.16
Map minimum: ..... 0
[1m(set-contour-level-absolute 0.30)[0m
[1m(n-chains 0)[0m
[1m(chain_id 0 0)[0m
[1m(chain-n-residues "A" 0)[0m
There are 97 residues in chain A
[1m(resname-from-serial-number 0 "A" 0)[0m
[1m(seqnum-from-serial-number 0 "A" 0)[0m
[1m(insertion-code-from-serial-number 0 "A" 0)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 1)[0m
[1m(seqnum-from-serial-number 0 "A" 1)[0m
[1m(insertion-code-from-serial-number 0 "A" 1)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 2)[0m
[1m(seqnum-from-serial-number 0 "A" 2)[0m
[1m(insertion-code-from-serial-number 0 "A" 2)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 3)[0m
[1m(seqnum-from-serial-number 0 "A" 3)[0m
[1m(insertion-code-from-serial-number 0 "A" 3)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 4)[0m
[1m(seqnum-from-serial-number 0 "A" 4)[0m
[1m(insertion-code-from-serial-number 0 "A" 4)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 5)[0m
[1m(seqnum-from-serial-number 0 "A" 5)[0m
[1m(insertion-code-from-serial-number 0 "A" 5)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 6)[0m
[1m(seqnum-from-serial-number 0 "A" 6)[0m
[1m(insertion-code-from-serial-number 0 "A" 6)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 7)[0m
[1m(seqnum-from-serial-number 0 "A" 7)[0m
[1m(insertion-code-from-serial-number 0 "A" 7)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 8)[0m
[1m(seqnum-from-serial-number 0 "A" 8)[0m
[1m(insertion-code-from-serial-number 0 "A" 8)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 9)[0m
[1m(seqnum-from-serial-number 0 "A" 9)[0m
[1m(insertion-code-from-serial-number 0 "A" 9)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 10)[0m
[1m(seqnum-from-serial-number 0 "A" 10)[0m
[1m(insertion-code-from-serial-number 0 "A" 10)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 11)[0m
[1m(seqnum-from-serial-number 0 "A" 11)[0m
[1m(insertion-code-from-serial-number 0 "A" 11)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 12)[0m
[1m(seqnum-from-serial-number 0 "A" 12)[0m
[1m(insertion-code-from-serial-number 0 "A" 12)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 13)[0m
[1m(seqnum-from-serial-number 0 "A" 13)[0m
[1m(insertion-code-from-serial-number 0 "A" 13)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 14)[0m
[1m(seqnum-from-serial-number 0 "A" 14)[0m
[1m(insertion-code-from-serial-number 0 "A" 14)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 15)[0m
[1m(seqnum-from-serial-number 0 "A" 15)[0m
[1m(insertion-code-from-serial-number 0 "A" 15)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 16)[0m
[1m(seqnum-from-serial-number 0 "A" 16)[0m
[1m(insertion-code-from-serial-number 0 "A" 16)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 17)[0m
[1m(seqnum-from-serial-number 0 "A" 17)[0m
[1m(insertion-code-from-serial-number 0 "A" 17)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 18)[0m
[1m(seqnum-from-serial-number 0 "A" 18)[0m
[1m(insertion-code-from-serial-number 0 "A" 18)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 19)[0m
[1m(seqnum-from-serial-number 0 "A" 19)[0m
[1m(insertion-code-from-serial-number 0 "A" 19)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 20)[0m
[1m(seqnum-from-serial-number 0 "A" 20)[0m
[1m(insertion-code-from-serial-number 0 "A" 20)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 21)[0m
[1m(seqnum-from-serial-number 0 "A" 21)[0m
[1m(insertion-code-from-serial-number 0 "A" 21)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 22)[0m
[1m(seqnum-from-serial-number 0 "A" 22)[0m
[1m(insertion-code-from-serial-number 0 "A" 22)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 23)[0m
[1m(seqnum-from-serial-number 0 "A" 23)[0m
[1m(insertion-code-from-serial-number 0 "A" 23)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 24)[0m
[1m(seqnum-from-serial-number 0 "A" 24)[0m
[1m(insertion-code-from-serial-number 0 "A" 24)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 25)[0m
[1m(seqnum-from-serial-number 0 "A" 25)[0m
[1m(insertion-code-from-serial-number 0 "A" 25)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 26)[0m
[1m(seqnum-from-serial-number 0 "A" 26)[0m
[1m(insertion-code-from-serial-number 0 "A" 26)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 27)[0m
[1m(seqnum-from-serial-number 0 "A" 27)[0m
[1m(insertion-code-from-serial-number 0 "A" 27)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 28)[0m
[1m(seqnum-from-serial-number 0 "A" 28)[0m
[1m(insertion-code-from-serial-number 0 "A" 28)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 29)[0m
[1m(seqnum-from-serial-number 0 "A" 29)[0m
[1m(insertion-code-from-serial-number 0 "A" 29)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 30)[0m
[1m(seqnum-from-serial-number 0 "A" 30)[0m
[1m(insertion-code-from-serial-number 0 "A" 30)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 31)[0m
[1m(seqnum-from-serial-number 0 "A" 31)[0m
[1m(insertion-code-from-serial-number 0 "A" 31)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 32)[0m
[1m(seqnum-from-serial-number 0 "A" 32)[0m
[1m(insertion-code-from-serial-number 0 "A" 32)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 33)[0m
[1m(seqnum-from-serial-number 0 "A" 33)[0m
[1m(insertion-code-from-serial-number 0 "A" 33)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 34)[0m
[1m(seqnum-from-serial-number 0 "A" 34)[0m
[1m(insertion-code-from-serial-number 0 "A" 34)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 35)[0m
[1m(seqnum-from-serial-number 0 "A" 35)[0m
[1m(insertion-code-from-serial-number 0 "A" 35)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 36)[0m
[1m(seqnum-from-serial-number 0 "A" 36)[0m
[1m(insertion-code-from-serial-number 0 "A" 36)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 37)[0m
[1m(seqnum-from-serial-number 0 "A" 37)[0m
[1m(insertion-code-from-serial-number 0 "A" 37)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 38)[0m
[1m(seqnum-from-serial-number 0 "A" 38)[0m
[1m(insertion-code-from-serial-number 0 "A" 38)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 39)[0m
[1m(seqnum-from-serial-number 0 "A" 39)[0m
[1m(insertion-code-from-serial-number 0 "A" 39)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 40)[0m
[1m(seqnum-from-serial-number 0 "A" 40)[0m
[1m(insertion-code-from-serial-number 0 "A" 40)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 41)[0m
[1m(seqnum-from-serial-number 0 "A" 41)[0m
[1m(insertion-code-from-serial-number 0 "A" 41)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 42)[0m
[1m(seqnum-from-serial-number 0 "A" 42)[0m
[1m(insertion-code-from-serial-number 0 "A" 42)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 43)[0m
[1m(seqnum-from-serial-number 0 "A" 43)[0m
[1m(insertion-code-from-serial-number 0 "A" 43)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 44)[0m
[1m(seqnum-from-serial-number 0 "A" 44)[0m
[1m(insertion-code-from-serial-number 0 "A" 44)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 45)[0m
[1m(seqnum-from-serial-number 0 "A" 45)[0m
[1m(insertion-code-from-serial-number 0 "A" 45)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 46)[0m
[1m(seqnum-from-serial-number 0 "A" 46)[0m
[1m(insertion-code-from-serial-number 0 "A" 46)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 47)[0m
[1m(seqnum-from-serial-number 0 "A" 47)[0m
[1m(insertion-code-from-serial-number 0 "A" 47)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 48)[0m
[1m(seqnum-from-serial-number 0 "A" 48)[0m
[1m(insertion-code-from-serial-number 0 "A" 48)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 49)[0m
[1m(seqnum-from-serial-number 0 "A" 49)[0m
[1m(insertion-code-from-serial-number 0 "A" 49)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 50)[0m
[1m(seqnum-from-serial-number 0 "A" 50)[0m
[1m(insertion-code-from-serial-number 0 "A" 50)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 51)[0m
[1m(seqnum-from-serial-number 0 "A" 51)[0m
[1m(insertion-code-from-serial-number 0 "A" 51)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 52)[0m
[1m(seqnum-from-serial-number 0 "A" 52)[0m
[1m(insertion-code-from-serial-number 0 "A" 52)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 53)[0m
[1m(seqnum-from-serial-number 0 "A" 53)[0m
[1m(insertion-code-from-serial-number 0 "A" 53)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 54)[0m
[1m(seqnum-from-serial-number 0 "A" 54)[0m
[1m(insertion-code-from-serial-number 0 "A" 54)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 55)[0m
[1m(seqnum-from-serial-number 0 "A" 55)[0m
[1m(insertion-code-from-serial-number 0 "A" 55)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 56)[0m
[1m(seqnum-from-serial-number 0 "A" 56)[0m
[1m(insertion-code-from-serial-number 0 "A" 56)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 57)[0m
[1m(seqnum-from-serial-number 0 "A" 57)[0m
[1m(insertion-code-from-serial-number 0 "A" 57)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 58)[0m
[1m(seqnum-from-serial-number 0 "A" 58)[0m
[1m(insertion-code-from-serial-number 0 "A" 58)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 59)[0m
[1m(seqnum-from-serial-number 0 "A" 59)[0m
[1m(insertion-code-from-serial-number 0 "A" 59)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 60)[0m
[1m(seqnum-from-serial-number 0 "A" 60)[0m
[1m(insertion-code-from-serial-number 0 "A" 60)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 61)[0m
[1m(seqnum-from-serial-number 0 "A" 61)[0m
[1m(insertion-code-from-serial-number 0 "A" 61)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 62)[0m
[1m(seqnum-from-serial-number 0 "A" 62)[0m
[1m(insertion-code-from-serial-number 0 "A" 62)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 63)[0m
[1m(seqnum-from-serial-number 0 "A" 63)[0m
[1m(insertion-code-from-serial-number 0 "A" 63)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 64)[0m
[1m(seqnum-from-serial-number 0 "A" 64)[0m
[1m(insertion-code-from-serial-number 0 "A" 64)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 65)[0m
[1m(seqnum-from-serial-number 0 "A" 65)[0m
[1m(insertion-code-from-serial-number 0 "A" 65)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 66)[0m
[1m(seqnum-from-serial-number 0 "A" 66)[0m
[1m(insertion-code-from-serial-number 0 "A" 66)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 67)[0m
[1m(seqnum-from-serial-number 0 "A" 67)[0m
[1m(insertion-code-from-serial-number 0 "A" 67)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 68)[0m
[1m(seqnum-from-serial-number 0 "A" 68)[0m
[1m(insertion-code-from-serial-number 0 "A" 68)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 69)[0m
[1m(seqnum-from-serial-number 0 "A" 69)[0m
[1m(insertion-code-from-serial-number 0 "A" 69)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 70)[0m
[1m(seqnum-from-serial-number 0 "A" 70)[0m
[1m(insertion-code-from-serial-number 0 "A" 70)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 71)[0m
[1m(seqnum-from-serial-number 0 "A" 71)[0m
[1m(insertion-code-from-serial-number 0 "A" 71)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 72)[0m
[1m(seqnum-from-serial-number 0 "A" 72)[0m
[1m(insertion-code-from-serial-number 0 "A" 72)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 73)[0m
[1m(seqnum-from-serial-number 0 "A" 73)[0m
[1m(insertion-code-from-serial-number 0 "A" 73)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 74)[0m
[1m(seqnum-from-serial-number 0 "A" 74)[0m
[1m(insertion-code-from-serial-number 0 "A" 74)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 75)[0m
[1m(seqnum-from-serial-number 0 "A" 75)[0m
[1m(insertion-code-from-serial-number 0 "A" 75)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 76)[0m
[1m(seqnum-from-serial-number 0 "A" 76)[0m
[1m(insertion-code-from-serial-number 0 "A" 76)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 77)[0m
[1m(seqnum-from-serial-number 0 "A" 77)[0m
[1m(insertion-code-from-serial-number 0 "A" 77)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 78)[0m
[1m(seqnum-from-serial-number 0 "A" 78)[0m
[1m(insertion-code-from-serial-number 0 "A" 78)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 79)[0m
[1m(seqnum-from-serial-number 0 "A" 79)[0m
[1m(insertion-code-from-serial-number 0 "A" 79)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 80)[0m
[1m(seqnum-from-serial-number 0 "A" 80)[0m
[1m(insertion-code-from-serial-number 0 "A" 80)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 81)[0m
[1m(seqnum-from-serial-number 0 "A" 81)[0m
[1m(insertion-code-from-serial-number 0 "A" 81)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 82)[0m
[1m(seqnum-from-serial-number 0 "A" 82)[0m
[1m(insertion-code-from-serial-number 0 "A" 82)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 83)[0m
[1m(seqnum-from-serial-number 0 "A" 83)[0m
[1m(insertion-code-from-serial-number 0 "A" 83)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 84)[0m
[1m(seqnum-from-serial-number 0 "A" 84)[0m
[1m(insertion-code-from-serial-number 0 "A" 84)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 85)[0m
[1m(seqnum-from-serial-number 0 "A" 85)[0m
[1m(insertion-code-from-serial-number 0 "A" 85)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 86)[0m
[1m(seqnum-from-serial-number 0 "A" 86)[0m
[1m(insertion-code-from-serial-number 0 "A" 86)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 87)[0m
[1m(seqnum-from-serial-number 0 "A" 87)[0m
[1m(insertion-code-from-serial-number 0 "A" 87)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 88)[0m
[1m(seqnum-from-serial-number 0 "A" 88)[0m
[1m(insertion-code-from-serial-number 0 "A" 88)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 89)[0m
[1m(seqnum-from-serial-number 0 "A" 89)[0m
[1m(insertion-code-from-serial-number 0 "A" 89)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 90)[0m
[1m(seqnum-from-serial-number 0 "A" 90)[0m
[1m(insertion-code-from-serial-number 0 "A" 90)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 91)[0m
[1m(seqnum-from-serial-number 0 "A" 91)[0m
[1m(insertion-code-from-serial-number 0 "A" 91)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 92)[0m
[1m(seqnum-from-serial-number 0 "A" 92)[0m
[1m(insertion-code-from-serial-number 0 "A" 92)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 93)[0m
[1m(seqnum-from-serial-number 0 "A" 93)[0m
[1m(insertion-code-from-serial-number 0 "A" 93)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 94)[0m
[1m(seqnum-from-serial-number 0 "A" 94)[0m
[1m(insertion-code-from-serial-number 0 "A" 94)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 95)[0m
[1m(seqnum-from-serial-number 0 "A" 95)[0m
[1m(insertion-code-from-serial-number 0 "A" 95)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 96)[0m
[1m(seqnum-from-serial-number 0 "A" 96)[0m
[1m(insertion-code-from-serial-number 0 "A" 96)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(write-pdb-file 0 "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb")[0m
[1m(close-molecule 0)[0m
[1m(close-molecule 1)[0m
[1m(stereo-mode-state)[0m
State file 0-coot.state.scm written.
[1m(stereo-mode-state)[0m
State file 0-coot.state.py written.
[1m(save-state)[0m
State file 0-coot-history.py written.
State file 0-coot-history.scm written.
Starting phenix.real_space_refine (version: 1.20)
on Fri Jun 9 14:26:00 2023 by webdklab
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb
Found real_map, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
resolution=3.7000
output.suffix=_phenix_refine
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
default_real_map = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
model {
file = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb"
}
default_model = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb"
}
resolution = 3.7000
output {
suffix = _phenix_refine
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.038
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.00s
Monomer Library directory:
"/apps/phenix/phenix-1.20-4459/modules/chem_data/mon_lib"
Total number of atoms: 2035
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2035
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 97, 2035
Classifications: {'RNA': 97}
Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 35, 'rna3p_pur': 1, 'rna2p_pyr': 60}
Link IDs: {'rna3p': 2, 'rna2p': 94}
Chain breaks: 20
Time building chain proxies: 0.42, per 1000 atoms: 0.21
Number of scatterers: 2035
At special positions: 0
Unit cell: (50, 58, 137, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
P 97 15.00
O 697 8.00
N 332 7.00
C 909 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.31
Conformation dependent library (CDL) restraints added in 4.5 milliseconds
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 0
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 0 sheets defined
0.0% alpha, 0.0% beta
15 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.17
Creating SS restraints...
No hydrogen bonds defined for protein.
Restraints generated for nucleic acids:
32 hydrogen bonds
38 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 0.13
Time building geometry restraints manager: 0.33 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.37: 624
1.37 - 1.55: 1428
1.55 - 1.72: 180
1.72 - 1.89: 10
1.89 - 2.07: 2
Bond restraints: 2244
Sorted by residual:
bond pdb="C1' U A 4 "
pdb="N1 U A 4 "
ideal model delta sigma weight residual
1.480 2.068 -0.588 1.50e-02 4.44e+03 1.54e+03
bond pdb="P C A 54 "
pdb="O5' C A 54 "
ideal model delta sigma weight residual
1.593 2.000 -0.407 1.50e-02 4.44e+03 7.35e+02
bond pdb="N1 G A 3 "
pdb="C2 G A 3 "
ideal model delta sigma weight residual
1.373 1.879 -0.506 2.00e-02 2.50e+03 6.40e+02
bond pdb="C2 C A 53 "
pdb="N3 C A 53 "
ideal model delta sigma weight residual
1.353 1.831 -0.478 2.00e-02 2.50e+03 5.72e+02
bond pdb="C6 G A 3 "
pdb="N1 G A 3 "
ideal model delta sigma weight residual
1.391 1.861 -0.470 2.00e-02 2.50e+03 5.52e+02
... (remaining 2239 not shown)
Histogram of bond angle deviations from ideal:
69.81 - 87.35: 52
87.35 - 104.90: 384
104.90 - 122.44: 2520
122.44 - 139.99: 479
139.99 - 157.54: 5
Bond angle restraints: 3440
Sorted by residual:
angle pdb="P C A 54 "
pdb="O5' C A 54 "
pdb="C5' C A 54 "
ideal model delta sigma weight residual
120.90 150.09 -29.19 1.50e+00 4.44e-01 3.79e+02
angle pdb="C2 U A 4 "
pdb="N1 U A 4 "
pdb="C6 U A 4 "
ideal model delta sigma weight residual
121.00 70.79 50.21 3.00e+00 1.11e-01 2.80e+02
angle pdb="OP1 C A 20 "
pdb="P C A 20 "
pdb="OP2 C A 20 "
ideal model delta sigma weight residual
119.60 77.12 42.48 3.00e+00 1.11e-01 2.01e+02
angle pdb="OP1 G A 52 "
pdb="P G A 52 "
pdb="OP2 G A 52 "
ideal model delta sigma weight residual
119.60 78.40 41.20 3.00e+00 1.11e-01 1.89e+02
angle pdb="C2' G A 3 "
pdb="C1' G A 3 "
pdb="N9 G A 3 "
ideal model delta sigma weight residual
112.00 131.74 -19.74 1.50e+00 4.44e-01 1.73e+02
... (remaining 3435 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.97: 846
35.97 - 71.95: 190
71.95 - 107.92: 48
107.92 - 143.89: 11
143.89 - 179.87: 6
Dihedral angle restraints: 1101
sinusoidal: 1101
harmonic: 0
Sorted by residual:
dihedral pdb="C4' G A 3 "
pdb="C3' G A 3 "
pdb="C2' G A 3 "
pdb="C1' G A 3 "
ideal model delta sinusoidal sigma weight residual
36.00 -30.56 66.56 1 8.00e+00 1.56e-02 9.03e+01
dihedral pdb="C4' U A 4 "
pdb="C3' U A 4 "
pdb="C2' U A 4 "
pdb="C1' U A 4 "
ideal model delta sinusoidal sigma weight residual
36.00 -24.80 60.80 1 8.00e+00 1.56e-02 7.68e+01
dihedral pdb="O4' G A 3 "
pdb="C2' G A 3 "
pdb="C1' G A 3 "
pdb="C3' G A 3 "
ideal model delta sinusoidal sigma weight residual
25.00 -35.29 60.29 1 8.00e+00 1.56e-02 7.57e+01
... (remaining 1098 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.741: 458
0.741 - 1.481: 25
1.481 - 2.221: 1
2.221 - 2.961: 0
2.961 - 3.702: 1
Chirality restraints: 485
Sorted by residual:
chirality pdb="C1' G A 3 "
pdb="O4' G A 3 "
pdb="C2' G A 3 "
pdb="N9 G A 3 "
both_signs ideal model delta sigma weight residual
False 2.46 -1.24 3.70 2.00e-01 2.50e+01 3.43e+02
chirality pdb="P A A 81 "
pdb="OP1 A A 81 "
pdb="OP2 A A 81 "
pdb="O5' A A 81 "
both_signs ideal model delta sigma weight residual
True 2.41 -0.83 1.58 2.00e-01 2.50e+01 6.26e+01
chirality pdb="P G A 37 "
pdb="OP1 G A 37 "
pdb="OP2 G A 37 "
pdb="O5' G A 37 "
both_signs ideal model delta sigma weight residual
True 2.41 -0.96 1.45 2.00e-01 2.50e+01 5.23e+01
... (remaining 482 not shown)
Planarity restraints: 97
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb="C1' G A 3 " -0.084 2.00e-02 2.50e+03 4.21e-02 5.31e+01
pdb="N9 G A 3 " 0.078 2.00e-02 2.50e+03
pdb="C8 G A 3 " 0.054 2.00e-02 2.50e+03
pdb="N7 G A 3 " 0.007 2.00e-02 2.50e+03
pdb="C5 G A 3 " -0.019 2.00e-02 2.50e+03
pdb="C6 G A 3 " -0.029 2.00e-02 2.50e+03
pdb="O6 G A 3 " 0.004 2.00e-02 2.50e+03
pdb="N1 G A 3 " -0.030 2.00e-02 2.50e+03
pdb="C2 G A 3 " 0.046 2.00e-02 2.50e+03
pdb="N2 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="N3 G A 3 " 0.003 2.00e-02 2.50e+03
pdb="C4 G A 3 " -0.031 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' U A 24 " 0.030 2.00e-02 2.50e+03 2.06e-02 9.54e+00
pdb="N1 U A 24 " -0.035 2.00e-02 2.50e+03
pdb="C2 U A 24 " 0.007 2.00e-02 2.50e+03
pdb="O2 U A 24 " -0.000 2.00e-02 2.50e+03
pdb="N3 U A 24 " -0.008 2.00e-02 2.50e+03
pdb="C4 U A 24 " -0.024 2.00e-02 2.50e+03
pdb="O4 U A 24 " 0.031 2.00e-02 2.50e+03
pdb="C5 U A 24 " 0.000 2.00e-02 2.50e+03
pdb="C6 U A 24 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' C A 13 " 0.024 2.00e-02 2.50e+03 1.58e-02 5.60e+00
pdb="N1 C A 13 " -0.029 2.00e-02 2.50e+03
pdb="C2 C A 13 " 0.003 2.00e-02 2.50e+03
pdb="O2 C A 13 " -0.003 2.00e-02 2.50e+03
pdb="N3 C A 13 " 0.006 2.00e-02 2.50e+03
pdb="C4 C A 13 " -0.021 2.00e-02 2.50e+03
pdb="N4 C A 13 " 0.018 2.00e-02 2.50e+03
pdb="C5 C A 13 " 0.002 2.00e-02 2.50e+03
pdb="C6 C A 13 " 0.000 2.00e-02 2.50e+03
... (remaining 94 not shown)
Histogram of nonbonded interaction distances:
1.68 - 2.32: 94
2.32 - 2.97: 1257
2.97 - 3.61: 3978
3.61 - 4.26: 5315
4.26 - 4.90: 7020
Nonbonded interactions: 17664
Sorted by model distance:
nonbonded pdb="N1 C A 53 "
pdb="O5' C A 54 "
model vdw
1.677 3.120
nonbonded pdb="N1 G A 3 "
pdb="N1 U A 4 "
model vdw
1.685 3.200
nonbonded pdb="N3 C A 53 "
pdb="O5' C A 54 "
model vdw
1.739 3.120
nonbonded pdb="C2 C A 53 "
pdb="O5' C A 54 "
model vdw
1.746 3.260
nonbonded pdb="C2 G A 3 "
pdb="N1 U A 4 "
model vdw
1.761 3.340
... (remaining 17659 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
P 97 5.49 5
C 909 2.51 5
N 332 2.21 5
O 697 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 5
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Write .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.540
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 1.000
Check model and map are aligned: 0.010
Convert atoms to be neutral: 0.010
Process input model: 2.860
Find NCS groups from input model: 0.010
Set up NCS constraints: 0.000
Set refine NCS operators: 0.000
Set scattering table: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:0.720
Set ADP refinement strategy: 0.000
Write .geo file: 1.170
Internal consistency checks: 0.000
Total: 6.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.588 2244 Z= 2.080
Angle : 5.098 50.215 3440 Z= 1.895
Chirality : 0.348 3.702 485
Planarity : 0.008 0.042 97
Dihedral : 34.403 179.867 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 89.43
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0176
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.6980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 6.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.6738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start: 0.2071
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.599 2244 Z= 2.064
Angle : 4.137 49.444 3440 Z= 1.568
Chirality : 0.451 3.878 485
Planarity : 0.007 0.032 97
Dihedral : 33.670 177.120 1101
Min Nonbonded Distance : 1.663
Molprobity Statistics.
All-atom Clashscore : 86.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.034
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0271
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.016
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0069
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 3.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start: 0.5577
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.598 2244 Z= 2.069
Angle : 4.156 49.090 3440 Z= 1.568
Chirality : 0.444 3.887 485
Planarity : 0.007 0.032 97
Dihedral : 33.481 173.787 1101
Min Nonbonded Distance : 1.670
Molprobity Statistics.
All-atom Clashscore : 92.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0175
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0064
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 40.0000
chunk 1 optimal weight: 0.6980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 3.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 8.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.9238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start: 0.6666
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.591 2244 Z= 2.065
Angle : 4.133 49.205 3440 Z= 1.564
Chirality : 0.446 3.905 485
Planarity : 0.007 0.033 97
Dihedral : 33.179 178.666 1101
Min Nonbonded Distance : 1.665
Molprobity Statistics.
All-atom Clashscore : 94.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0176
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 1.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 0.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 4.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7490
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start: 0.8383
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.585 2244 Z= 2.062
Angle : 3.950 49.218 3440 Z= 1.504
Chirality : 0.446 3.954 485
Planarity : 0.007 0.028 97
Dihedral : 32.960 177.589 1101
Min Nonbonded Distance : 1.666
Molprobity Statistics.
All-atom Clashscore : 88.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0170
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0061
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 40.0000
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 5.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.107818 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.095179 restraints weight = 11644.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.096973 restraints weight = 4989.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.098160 restraints weight = 2997.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start: 0.8868
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.597 2244 Z= 2.070
Angle : 3.939 49.217 3440 Z= 1.500
Chirality : 0.447 3.891 485
Planarity : 0.007 0.031 97
Dihedral : 32.981 178.740 1101
Min Nonbonded Distance : 1.666
Molprobity Statistics.
All-atom Clashscore : 94.35
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
===============================================================================
Job complete
usr+sys time: 145.60 seconds
wall clock time: 4 minutes 32.11 seconds (272.11 seconds total)
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.167250633239746
dmean : 5.7266399380750954e-05
ispg : 1
nsymbt : 0
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exttyp : b''
nversion : 20141
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map : b'MAP '
machst : [68 68 0 0]
rms : 0.023769386112689972
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:59 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 86 isolated grid points
we have 0/174 base assignment outside safe range: 0.000
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_assignsugar_combine created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq created
we have 1/122 base assignment outside safe range: 0.008
we have 1/122 base assignment outside safe range: 0.008
only apply geometry constraints for dynamic programming
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0 created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0/path_order created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0/path_reverse_order created
geometrical based dp finished selecting ldp for atomic modeling
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Path_Atomic_Frags created
duplicate use of 13/98 pho positions in atomic
revise 25/98 pho positions in atomic
{3, 4, 6, 7, 8, 10, 12, 13, 21, 33, 34, 37, 38, 39, 41, 42, 45, 46, 54, 55, 56, 59, 60, 61, 99}
previous loc [141.22828214631141, 114.06837996436745, 101.35129613280449] updated loc: [141.22828214631141, 114.06837996436745, 101.35129613280449]
previous loc [117.78454159852292, 129.18897958649018, 156.73330225140765] updated loc: [117.90138026042874, 131.23901906657989, 155.40754600245518]
previous loc [117.78454159852292, 129.18897958649018, 156.73330225140765] updated loc: [117.78454159852292, 129.18897958649018, 156.73330225140765]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [136.87420336217642, 133.7489795495849, 170.55259591110692] updated loc: [136.87420336217642, 133.7489795495849, 170.55259591110692]
previous loc [136.87420336217642, 133.7489795495849, 170.55259591110692] updated loc: [136.87420336217642, 133.7489795495849, 170.55259591110692]
previous loc [126.66219761035069, 138.1737504527791, 181.89940763032868] updated loc: [128.4402524368203, 140.18530774000502, 179.2941443882781]
previous loc [126.66219761035069, 138.1737504527791, 181.89940763032868] updated loc: [126.27207221165374, 135.6400451342626, 183.4575478552197]
previous loc [141.8872530017751, 131.2376876647608, 177.46735245256994] updated loc: [141.38606830362136, 134.0230962905337, 180.1413201291402]
duplicate use of 5/98 pho positions in atomic
round 2 we still put 3 points into clear set
clearning changed 181 to 178 frag info
Reflection detected
Reflection detected
use pho situation 6
Reflection detected
use pho situation 2
use pho situation 7
Reflection detected
use pho situation 6
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
Reflection detected
use pho situation 7
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
use pho situation 5
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 2
use pho situation 7
use pho situation 6
Reflection detected
use pho situation 1
use pho situation 2
Reflection detected
use pho situation 5
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 2
Reflection detected
use pho situation 7
Reflection detected
Reflection detected
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 2
use pho situation 7
Reflection detected
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
use pho situation 9
Reflection detected
we have 94/98 atomic build upon pho atoms
!!!parsing fasta input failed, we can not output structures considering sequence assignment!!!
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
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b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
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nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
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/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output created
please check final refined atomic structure in /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle3.pdb
You can also check other refined output here /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output
INFO : CryoREAD Done
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/ existed
Origin: (0., 0., 0.)
Previous voxel size: 1.059999942779541
Previouse size: (256, 256, 256) Current map size: 271 271 271
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extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/1st_stage_detection created
map density range: 0.000000 3.159605
map hist log percentage 98: 2.5908763
detected mode mapc 1, mapr 2, maps 3
Origin: [0.0, 0.0, 0.0]
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/1st_stage_detection/Input created
given contour 0.300000
revised contour 0.115791
In total we prepared 1103 boxes as input
model loading: <All keys matched successfully>
#Eval:[ 0/276] data_time 0.168809 (0.168809) train_time 1.388435 (1.388435)
0 classes already detected 15 voxels
1 classes already detected 0 voxels
2 classes already detected 0 voxels
3 classes already detected 3810 voxels
#Eval:[ 1/276] data_time 0.001800 (0.085305) train_time 1.142597 (1.265516)
#Eval:[ 2/276] data_time 0.001034 (0.057215) train_time 1.145248 (1.225426)
#Eval:[ 3/276] data_time 0.001642 (0.043322) train_time 1.150283 (1.206641)
#Eval:[ 4/276] data_time 0.002274 (0.035112) train_time 1.150473 (1.195407)
#Eval:[ 5/276] data_time 0.002148 (0.029618) train_time 1.154119 (1.188526)
#Eval:[ 6/276] data_time 0.000574 (0.025469) train_time 1.151014 (1.183167)
#Eval:[ 7/276] data_time 0.000585 (0.022358) train_time 1.144880 (1.178381)
#Eval:[ 8/276] data_time 0.001362 (0.020025) train_time 1.147862 (1.174990)
#Eval:[ 9/276] data_time 0.001448 (0.018168) train_time 1.145905 (1.172082)
#Eval:[ 10/276] data_time 0.001487 (0.016651) train_time 1.146673 (1.169772)
#Eval:[ 11/276] data_time 0.001405 (0.015381) train_time 1.148096 (1.167965)
#Eval:[ 12/276] data_time 0.001482 (0.014311) train_time 1.147398 (1.166383)
#Eval:[ 13/276] data_time 0.001422 (0.013391) train_time 1.147236 (1.165016)
#Eval:[ 14/276] data_time 0.001358 (0.012589) train_time 1.147999 (1.163881)
#Eval:[ 15/276] data_time 0.001378 (0.011888) train_time 1.148555 (1.162923)
#Eval:[ 16/276] data_time 0.001462 (0.011275) train_time 1.150055 (1.162166)
#Eval:[ 17/276] data_time 0.001388 (0.010725) train_time 1.159393 (1.162012)
#Eval:[ 18/276] data_time 0.001527 (0.010241) train_time 1.151634 (1.161466)
#Eval:[ 19/276] data_time 0.001433 (0.009801) train_time 1.153358 (1.161061)
#Eval:[ 20/276] data_time 0.001433 (0.009402) train_time 1.153656 (1.160708)
#Eval:[ 21/276] data_time 0.001484 (0.009042) train_time 1.154579 (1.160429)
#Eval:[ 22/276] data_time 0.001504 (0.008715) train_time 1.153544 (1.160130)
#Eval:[ 23/276] data_time 0.001621 (0.008419) train_time 1.154637 (1.159901)
#Eval:[ 24/276] data_time 0.001446 (0.008140) train_time 1.152529 (1.159606)
#Eval:[ 25/276] data_time 0.001455 (0.007883) train_time 1.155627 (1.159453)
#Eval:[ 26/276] data_time 0.001451 (0.007645) train_time 1.154473 (1.159269)
#Eval:[ 27/276] data_time 0.001602 (0.007429) train_time 1.155115 (1.159120)
#Eval:[ 28/276] data_time 0.001451 (0.007223) train_time 1.155848 (1.159008)
#Eval:[ 29/276] data_time 0.001482 (0.007032) train_time 1.155759 (1.158899)
#Eval:[ 30/276] data_time 0.001456 (0.006852) train_time 1.167185 (1.159167)
#Eval:[ 31/276] data_time 0.001443 (0.006683) train_time 1.165138 (1.159353)
#Eval:[ 32/276] data_time 0.001341 (0.006521) train_time 1.157462 (1.159296)
#Eval:[ 33/276] data_time 0.001621 (0.006377) train_time 1.158143 (1.159262)
#Eval:[ 34/276] data_time 0.001446 (0.006236) train_time 1.158155 (1.159230)
#Eval:[ 35/276] data_time 0.001626 (0.006108) train_time 1.162202 (1.159313)
#Eval:[ 36/276] data_time 0.001382 (0.005980) train_time 1.159826 (1.159327)
#Eval:[ 37/276] data_time 0.001299 (0.005857) train_time 1.159303 (1.159326)
#Eval:[ 38/276] data_time 0.001420 (0.005743) train_time 1.159130 (1.159321)
#Eval:[ 39/276] data_time 0.001440 (0.005635) train_time 1.160742 (1.159357)
#Eval:[ 40/276] data_time 0.001653 (0.005538) train_time 1.163716 (1.159463)
#Eval:[ 41/276] data_time 0.001439 (0.005441) train_time 1.161656 (1.159515)
#Eval:[ 42/276] data_time 0.001489 (0.005349) train_time 1.160494 (1.159538)
#Eval:[ 43/276] data_time 0.001370 (0.005258) train_time 1.163268 (1.159623)
#Eval:[ 44/276] data_time 0.001667 (0.005179) train_time 1.162032 (1.159676)
#Eval:[ 45/276] data_time 0.001460 (0.005098) train_time 1.162102 (1.159729)
#Eval:[ 46/276] data_time 0.001411 (0.005019) train_time 1.161756 (1.159772)
#Eval:[ 47/276] data_time 0.001497 (0.004946) train_time 1.132329 (1.159200)
#Eval:[ 48/276] data_time 0.001388 (0.004873) train_time 1.131824 (1.158642)
#Eval:[ 49/276] data_time 0.001457 (0.004805) train_time 1.132567 (1.158120)
#Eval:[ 50/276] data_time 0.001491 (0.004740) train_time 1.148992 (1.157941)
#Eval:[ 51/276] data_time 0.001675 (0.004681) train_time 1.160306 (1.157987)
#Eval:[ 52/276] data_time 0.001243 (0.004616) train_time 1.169487 (1.158204)
#Eval:[ 53/276] data_time 0.001450 (0.004558) train_time 1.304640 (1.160915)
#Eval:[ 54/276] data_time 0.001439 (0.004501) train_time 1.628127 (1.169410)
#Eval:[ 55/276] data_time 0.001350 (0.004445) train_time 1.631440 (1.177661)
#Eval:[ 56/276] data_time 0.001385 (0.004391) train_time 1.636396 (1.185709)
#Eval:[ 57/276] data_time 0.001407 (0.004339) train_time 1.627539 (1.193326)
#Eval:[ 58/276] data_time 0.001415 (0.004290) train_time 1.635790 (1.200826)
#Eval:[ 59/276] data_time 0.001569 (0.004245) train_time 1.626545 (1.207921)
#Eval:[ 60/276] data_time 0.001378 (0.004198) train_time 1.636417 (1.214946)
#Eval:[ 61/276] data_time 0.001475 (0.004154) train_time 1.632172 (1.221675)
#Eval:[ 62/276] data_time 0.001436 (0.004111) train_time 1.629753 (1.228153)
#Eval:[ 63/276] data_time 0.001650 (0.004072) train_time 1.631035 (1.234448)
#Eval:[ 64/276] data_time 0.001606 (0.004034) train_time 1.639992 (1.240687)
#Eval:[ 65/276] data_time 0.001624 (0.003998) train_time 1.633433 (1.246637)
#Eval:[ 66/276] data_time 0.001456 (0.003960) train_time 1.633184 (1.252407)
#Eval:[ 67/276] data_time 0.001518 (0.003924) train_time 1.632929 (1.258003)
#Eval:[ 68/276] data_time 0.001454 (0.003888) train_time 1.639790 (1.263536)
#Eval:[ 69/276] data_time 0.001635 (0.003856) train_time 1.634365 (1.268833)
#Eval:[ 70/276] data_time 0.001541 (0.003823) train_time 1.638146 (1.274035)
#Eval:[ 71/276] data_time 0.001598 (0.003792) train_time 1.637392 (1.279082)
#Eval:[ 72/276] data_time 0.001631 (0.003763) train_time 1.635152 (1.283959)
#Eval:[ 73/276] data_time 0.001425 (0.003731) train_time 1.637983 (1.288743)
#Eval:[ 74/276] data_time 0.001464 (0.003701) train_time 1.636283 (1.293377)
#Eval:[ 75/276] data_time 0.001661 (0.003674) train_time 1.635507 (1.297879)
#Eval:[ 76/276] data_time 0.001356 (0.003644) train_time 1.639899 (1.302321)
#Eval:[ 77/276] data_time 0.001368 (0.003615) train_time 1.628958 (1.306508)
#Eval:[ 78/276] data_time 0.001401 (0.003587) train_time 1.639042 (1.310718)
#Eval:[ 79/276] data_time 0.001657 (0.003563) train_time 1.636012 (1.314784)
#Eval:[ 80/276] data_time 0.001355 (0.003535) train_time 1.646013 (1.318873)
#Eval:[ 81/276] data_time 0.001458 (0.003510) train_time 1.640026 (1.322790)
#Eval:[ 82/276] data_time 0.001467 (0.003485) train_time 1.647643 (1.326704)
#Eval:[ 83/276] data_time 0.001696 (0.003464) train_time 1.647898 (1.330527)
#Eval:[ 84/276] data_time 0.001475 (0.003441) train_time 1.644312 (1.334219)
#Eval:[ 85/276] data_time 0.001664 (0.003420) train_time 1.635035 (1.337717)
#Eval:[ 86/276] data_time 0.001499 (0.003398) train_time 1.645303 (1.341252)
#Eval:[ 87/276] data_time 0.001784 (0.003380) train_time 1.636822 (1.344611)
#Eval:[ 88/276] data_time 0.001518 (0.003359) train_time 1.641252 (1.347944)
#Eval:[ 89/276] data_time 0.001662 (0.003340) train_time 1.641771 (1.351209)
#Eval:[ 90/276] data_time 0.001492 (0.003320) train_time 1.645522 (1.354443)
#Eval:[ 91/276] data_time 0.001691 (0.003302) train_time 1.641578 (1.357564)
#Eval:[ 92/276] data_time 0.001644 (0.003284) train_time 1.639827 (1.360599)
#Eval:[ 93/276] data_time 0.001394 (0.003264) train_time 1.643160 (1.363605)
#Eval:[ 94/276] data_time 0.001549 (0.003246) train_time 1.649767 (1.366617)
#Eval:[ 95/276] data_time 0.001640 (0.003229) train_time 1.639071 (1.369455)
#Eval:[ 96/276] data_time 0.001591 (0.003212) train_time 1.643082 (1.372276)
#Eval:[ 97/276] data_time 0.001682 (0.003197) train_time 1.648361 (1.375093)
#Eval:[ 98/276] data_time 0.001448 (0.003179) train_time 1.642248 (1.377792)
#Eval:[ 99/276] data_time 0.001492 (0.003162) train_time 1.644391 (1.380458)
#Eval:[100/276] data_time 0.001421 (0.003145) train_time 1.652005 (1.383147)
#Eval:[101/276] data_time 0.001588 (0.003130) train_time 1.659935 (1.385860)
#Eval:[102/276] data_time 0.001522 (0.003114) train_time 1.649109 (1.388416)
#Eval:[103/276] data_time 0.001658 (0.003100) train_time 1.644192 (1.390875)
#Eval:[104/276] data_time 0.001415 (0.003084) train_time 1.646733 (1.393312)
#Eval:[105/276] data_time 0.001620 (0.003070) train_time 1.649866 (1.395732)
#Eval:[106/276] data_time 0.001527 (0.003056) train_time 1.640135 (1.398017)
#Eval:[107/276] data_time 0.001662 (0.003043) train_time 1.648204 (1.400333)
#Eval:[108/276] data_time 0.001507 (0.003029) train_time 1.644221 (1.402571)
#Eval:[109/276] data_time 0.001640 (0.003016) train_time 1.651451 (1.404833)
#Eval:[110/276] data_time 0.001461 (0.003002) train_time 1.645563 (1.407002)
#Eval:[111/276] data_time 0.001663 (0.002990) train_time 1.646295 (1.409138)
#Eval:[112/276] data_time 0.001484 (0.002977) train_time 1.651000 (1.411279)
#Eval:[113/276] data_time 0.001626 (0.002965) train_time 1.648634 (1.413361)
#Eval:[114/276] data_time 0.001473 (0.002952) train_time 1.644008 (1.415367)
#Eval:[115/276] data_time 0.001632 (0.002941) train_time 1.649377 (1.417384)
#Eval:[116/276] data_time 0.001682 (0.002930) train_time 1.665218 (1.419502)
#Eval:[117/276] data_time 0.001482 (0.002918) train_time 1.658849 (1.421530)
#Eval:[118/276] data_time 0.001456 (0.002905) train_time 1.645772 (1.423415)
#Eval:[119/276] data_time 0.001620 (0.002895) train_time 1.647531 (1.425282)
#Eval:[120/276] data_time 0.001622 (0.002884) train_time 1.647425 (1.427118)
#Eval:[121/276] data_time 0.001478 (0.002873) train_time 1.646744 (1.428919)
#Eval:[122/276] data_time 0.001428 (0.002861) train_time 1.645391 (1.430678)
#Eval:[123/276] data_time 0.001395 (0.002849) train_time 1.650068 (1.432448)
#Eval:[124/276] data_time 0.001464 (0.002838) train_time 1.651278 (1.434198)
#Eval:[125/276] data_time 0.001480 (0.002827) train_time 1.646598 (1.435884)
#Eval:[126/276] data_time 0.001454 (0.002816) train_time 1.647682 (1.437552)
#Eval:[127/276] data_time 0.001546 (0.002806) train_time 1.653528 (1.439239)
#Eval:[128/276] data_time 0.001498 (0.002796) train_time 1.645381 (1.440837)
#Eval:[129/276] data_time 0.001564 (0.002787) train_time 1.644861 (1.442407)
#Eval:[130/276] data_time 0.001423 (0.002776) train_time 1.651622 (1.444004)
#Eval:[131/276] data_time 0.001677 (0.002768) train_time 1.652293 (1.445582)
#Eval:[132/276] data_time 0.001357 (0.002757) train_time 1.650806 (1.447125)
#Eval:[133/276] data_time 0.001448 (0.002748) train_time 1.649523 (1.448635)
#Eval:[134/276] data_time 0.001496 (0.002738) train_time 1.646289 (1.450099)
#Eval:[135/276] data_time 0.001459 (0.002729) train_time 1.653949 (1.451598)
#Eval:[136/276] data_time 0.001486 (0.002720) train_time 1.646991 (1.453024)
#Eval:[137/276] data_time 0.001459 (0.002711) train_time 1.647745 (1.454435)
#Eval:[138/276] data_time 0.001475 (0.002702) train_time 1.652427 (1.455860)
#Eval:[139/276] data_time 0.001481 (0.002693) train_time 1.649833 (1.457245)
#Eval:[140/276] data_time 0.001468 (0.002684) train_time 1.648769 (1.458604)
#Eval:[141/276] data_time 0.001275 (0.002675) train_time 1.650670 (1.459956)
#Eval:[142/276] data_time 0.001900 (0.002669) train_time 1.647097 (1.461265)
#Eval:[143/276] data_time 0.001666 (0.002662) train_time 1.650956 (1.462582)
#Eval:[144/276] data_time 0.001436 (0.002654) train_time 1.655115 (1.463910)
#Eval:[145/276] data_time 0.001449 (0.002645) train_time 1.646806 (1.465163)
#Eval:[146/276] data_time 0.001501 (0.002638) train_time 1.648988 (1.466413)
#Eval:[147/276] data_time 0.001682 (0.002631) train_time 1.654251 (1.467682)
#Eval:[148/276] data_time 0.001613 (0.002624) train_time 1.650162 (1.468907)
#Eval:[149/276] data_time 0.001454 (0.002617) train_time 1.650058 (1.470115)
#Eval:[150/276] data_time 0.001518 (0.002609) train_time 1.656691 (1.471350)
#Eval:[151/276] data_time 0.001713 (0.002603) train_time 1.648989 (1.472519)
#Eval:[152/276] data_time 0.001395 (0.002595) train_time 1.645002 (1.473646)
#Eval:[153/276] data_time 0.001235 (0.002587) train_time 1.655208 (1.474825)
#Eval:[154/276] data_time 0.001450 (0.002579) train_time 1.643351 (1.475913)
#Eval:[155/276] data_time 0.001485 (0.002572) train_time 1.651629 (1.477039)
#Eval:[156/276] data_time 0.001678 (0.002567) train_time 1.653109 (1.478160)
#Eval:[157/276] data_time 0.001486 (0.002560) train_time 1.647948 (1.479235)
#Eval:[158/276] data_time 0.001636 (0.002554) train_time 1.650551 (1.480312)
#Eval:[159/276] data_time 0.001448 (0.002547) train_time 1.654900 (1.481404)
#Eval:[160/276] data_time 0.001483 (0.002540) train_time 1.650470 (1.482454)
#Eval:[161/276] data_time 0.001475 (0.002534) train_time 1.651929 (1.483500)
#Eval:[162/276] data_time 0.001525 (0.002528) train_time 1.651984 (1.484533)
#Eval:[163/276] data_time 0.001683 (0.002523) train_time 1.654110 (1.485568)
#Eval:[164/276] data_time 0.001493 (0.002516) train_time 1.643530 (1.486525)
#Eval:[165/276] data_time 0.001452 (0.002510) train_time 1.648796 (1.487502)
#Eval:[166/276] data_time 0.001556 (0.002504) train_time 1.658563 (1.488527)
#Eval:[167/276] data_time 0.001614 (0.002499) train_time 1.656322 (1.489525)
#Eval:[168/276] data_time 0.001623 (0.002494) train_time 1.655312 (1.490506)
#Eval:[169/276] data_time 0.001389 (0.002487) train_time 1.654980 (1.491474)
#Eval:[170/276] data_time 0.001582 (0.002482) train_time 1.659694 (1.492458)
#Eval:[171/276] data_time 0.001486 (0.002476) train_time 1.654384 (1.493399)
#Eval:[172/276] data_time 0.001383 (0.002470) train_time 1.656315 (1.494341)
#Eval:[173/276] data_time 0.001378 (0.002464) train_time 1.658087 (1.495282)
#Eval:[174/276] data_time 0.001498 (0.002458) train_time 1.662695 (1.496239)
#Eval:[175/276] data_time 0.001540 (0.002453) train_time 1.650927 (1.497117)
#Eval:[176/276] data_time 0.001642 (0.002448) train_time 1.656047 (1.498015)
#Eval:[177/276] data_time 0.001482 (0.002443) train_time 1.659915 (1.498925)
#Eval:[178/276] data_time 0.001479 (0.002437) train_time 1.654346 (1.499793)
#Eval:[179/276] data_time 0.001504 (0.002432) train_time 1.657459 (1.500669)
#Eval:[180/276] data_time 0.001498 (0.002427) train_time 1.653902 (1.501516)
#Eval:[181/276] data_time 0.001482 (0.002422) train_time 1.658445 (1.502378)
#Eval:[182/276] data_time 0.001651 (0.002418) train_time 1.655147 (1.503213)
#Eval:[183/276] data_time 0.001519 (0.002413) train_time 1.654359 (1.504034)
#Eval:[184/276] data_time 0.001683 (0.002409) train_time 1.656559 (1.504859)
#Eval:[185/276] data_time 0.001453 (0.002404) train_time 1.657841 (1.505681)
#Eval:[186/276] data_time 0.001521 (0.002399) train_time 1.651058 (1.506459)
#Eval:[187/276] data_time 0.001615 (0.002395) train_time 1.670264 (1.507330)
#Eval:[188/276] data_time 0.001508 (0.002390) train_time 1.669309 (1.508187)
#Eval:[189/276] data_time 0.001513 (0.002385) train_time 1.660786 (1.508990)
#Eval:[190/276] data_time 0.001613 (0.002381) train_time 1.655097 (1.509755)
#Eval:[191/276] data_time 0.001670 (0.002378) train_time 1.657459 (1.510524)
#Eval:[192/276] data_time 0.001852 (0.002375) train_time 1.659244 (1.511295)
#Eval:[193/276] data_time 0.001410 (0.002370) train_time 1.657641 (1.512049)
#Eval:[194/276] data_time 0.001478 (0.002365) train_time 1.655119 (1.512783)
#Eval:[195/276] data_time 0.001644 (0.002362) train_time 1.656252 (1.513515)
#Eval:[196/276] data_time 0.001661 (0.002358) train_time 1.661608 (1.514267)
#Eval:[197/276] data_time 0.001470 (0.002354) train_time 1.661400 (1.515010)
#Eval:[198/276] data_time 0.001535 (0.002350) train_time 1.656368 (1.515720)
#Eval:[199/276] data_time 0.001564 (0.002346) train_time 1.657504 (1.516429)
#Eval:[200/276] data_time 0.001424 (0.002341) train_time 1.657910 (1.517133)
#Eval:[201/276] data_time 0.001456 (0.002337) train_time 1.656127 (1.517821)
#Eval:[202/276] data_time 0.001385 (0.002332) train_time 1.657127 (1.518507)
#Eval:[203/276] data_time 0.001522 (0.002328) train_time 1.658980 (1.519196)
#Eval:[204/276] data_time 0.001471 (0.002324) train_time 1.662282 (1.519894)
#Eval:[205/276] data_time 0.001523 (0.002320) train_time 1.657882 (1.520564)
#Eval:[206/276] data_time 0.001369 (0.002315) train_time 1.656820 (1.521222)
#Eval:[207/276] data_time 0.001465 (0.002311) train_time 1.655184 (1.521866)
#Eval:[208/276] data_time 0.001539 (0.002308) train_time 1.666908 (1.522560)
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extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.012897069565951824
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:59:32 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/2nd_stage_detection created
map density range: 0.000000 3.159605
map hist log percentage 98: 2.5908763
detected mode mapc 1, mapr 2, maps 3
Origin: [0.0, 0.0, 0.0]
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/2nd_stage_detection/Input created
given contour 0.300000
revised contour 0.115791
in 2nd stage, in total we have 900 boxes
model loading: <All keys matched successfully>
#Eval:[ 0/225] data_time 0.353324 (0.353324) train_time 1.021894 (1.021894)
0 classes already detected 724 voxels
1 classes already detected 359 voxels
2 classes already detected 0 voxels
3 classes already detected 2 voxels
4 classes already detected 36 voxels
5 classes already detected 128 voxels
6 classes already detected 29879 voxels
7 classes already detected 935 voxels
#Eval:[ 1/225] data_time 0.222827 (0.288076) train_time 0.898544 (0.960219)
#Eval:[ 2/225] data_time 0.038179 (0.204777) train_time 0.776937 (0.899125)
#Eval:[ 3/225] data_time 0.037856 (0.163047) train_time 0.787261 (0.871159)
#Eval:[ 4/225] data_time 0.040595 (0.138556) train_time 0.791972 (0.855322)
#Eval:[ 5/225] data_time 0.040988 (0.122295) train_time 0.797586 (0.845699)
#Eval:[ 6/225] data_time 0.040360 (0.110590) train_time 0.789036 (0.837604)
#Eval:[ 7/225] data_time 0.039896 (0.101753) train_time 0.791974 (0.831900)
#Eval:[ 8/225] data_time 0.040278 (0.094923) train_time 0.790321 (0.827281)
#Eval:[ 9/225] data_time 0.041770 (0.089607) train_time 0.796901 (0.824243)
#Eval:[ 10/225] data_time 0.040153 (0.085111) train_time 0.792347 (0.821343)
#Eval:[ 11/225] data_time 0.039981 (0.081351) train_time 0.786901 (0.818473)
#Eval:[ 12/225] data_time 0.040867 (0.078236) train_time 0.792876 (0.816504)
#Eval:[ 13/225] data_time 0.040468 (0.075539) train_time 0.798477 (0.815216)
#Eval:[ 14/225] data_time 0.041767 (0.073287) train_time 0.799623 (0.814177)
#Eval:[ 15/225] data_time 0.040311 (0.071226) train_time 0.785644 (0.812393)
#Eval:[ 16/225] data_time 0.040268 (0.069405) train_time 0.797111 (0.811494)
#Eval:[ 17/225] data_time 0.039881 (0.067765) train_time 0.798075 (0.810749)
#Eval:[ 18/225] data_time 0.040542 (0.066332) train_time 0.802576 (0.810319)
#Eval:[ 19/225] data_time 0.039582 (0.064995) train_time 0.788466 (0.809226)
#Eval:[ 20/225] data_time 0.040563 (0.063831) train_time 0.796365 (0.808614)
#Eval:[ 21/225] data_time 0.040506 (0.062771) train_time 0.795652 (0.808025)
#Eval:[ 22/225] data_time 0.040458 (0.061801) train_time 0.797857 (0.807582)
#Eval:[ 23/225] data_time 0.040882 (0.060929) train_time 0.797897 (0.807179)
#Eval:[ 24/225] data_time 0.040913 (0.060129) train_time 0.798708 (0.806840)
#Eval:[ 25/225] data_time 0.040960 (0.059391) train_time 0.803163 (0.806699)
#Eval:[ 26/225] data_time 0.040093 (0.058677) train_time 0.799866 (0.806446)
#Eval:[ 27/225] data_time 0.039694 (0.057999) train_time 0.797520 (0.806127)
#Eval:[ 28/225] data_time 0.039761 (0.057370) train_time 0.800132 (0.805920)
#Eval:[ 29/225] data_time 0.040533 (0.056809) train_time 0.799073 (0.805692)
#Eval:[ 30/225] data_time 0.040257 (0.056275) train_time 0.806425 (0.805716)
#Eval:[ 31/225] data_time 0.039992 (0.055766) train_time 0.801387 (0.805580)
#Eval:[ 32/225] data_time 0.040647 (0.055308) train_time 0.805682 (0.805583)
#Eval:[ 33/225] data_time 0.040515 (0.054873) train_time 0.801444 (0.805462)
#Eval:[ 34/225] data_time 0.041032 (0.054477) train_time 0.811721 (0.805640)
#Eval:[ 35/225] data_time 0.040896 (0.054100) train_time 0.803612 (0.805584)
#Eval:[ 36/225] data_time 0.040744 (0.053739) train_time 0.809601 (0.805693)
#Eval:[ 37/225] data_time 0.041418 (0.053415) train_time 0.805974 (0.805700)
#Eval:[ 38/225] data_time 0.040259 (0.053077) train_time 0.810290 (0.805818)
#Eval:[ 39/225] data_time 0.041094 (0.052778) train_time 0.803531 (0.805761)
#Eval:[ 40/225] data_time 0.039910 (0.052464) train_time 0.807249 (0.805797)
#Eval:[ 41/225] data_time 0.040536 (0.052180) train_time 0.806144 (0.805805)
#Eval:[ 42/225] data_time 0.042400 (0.051952) train_time 0.807435 (0.805843)
#Eval:[ 43/225] data_time 0.043432 (0.051759) train_time 0.811019 (0.805961)
#Eval:[ 44/225] data_time 0.041226 (0.051525) train_time 0.807243 (0.805989)
#Eval:[ 45/225] data_time 0.040811 (0.051292) train_time 0.810134 (0.806079)
#Eval:[ 46/225] data_time 0.041412 (0.051082) train_time 0.809040 (0.806142)
#Eval:[ 47/225] data_time 0.041421 (0.050880) train_time 0.811074 (0.806245)
#Eval:[ 48/225] data_time 0.040816 (0.050675) train_time 0.808080 (0.806282)
#Eval:[ 49/225] data_time 0.041842 (0.050498) train_time 0.819847 (0.806554)
#Eval:[ 50/225] data_time 0.040665 (0.050306) train_time 0.804493 (0.806513)
#Eval:[ 51/225] data_time 0.040511 (0.050117) train_time 0.817381 (0.806722)
#Eval:[ 52/225] data_time 0.044540 (0.050012) train_time 0.810324 (0.806790)
#Eval:[ 53/225] data_time 0.040196 (0.049830) train_time 0.811689 (0.806881)
#Eval:[ 54/225] data_time 0.040613 (0.049663) train_time 0.807991 (0.806901)
#Eval:[ 55/225] data_time 0.041492 (0.049517) train_time 0.812014 (0.806993)
#Eval:[ 56/225] data_time 0.039906 (0.049348) train_time 0.803624 (0.806933)
#Eval:[ 57/225] data_time 0.044075 (0.049257) train_time 0.814005 (0.807055)
#Eval:[ 58/225] data_time 0.040814 (0.049114) train_time 0.805577 (0.807030)
#Eval:[ 59/225] data_time 0.040640 (0.048973) train_time 0.808917 (0.807062)
#Eval:[ 60/225] data_time 0.040619 (0.048836) train_time 0.807464 (0.807068)
#Eval:[ 61/225] data_time 0.042691 (0.048737) train_time 0.813154 (0.807166)
#Eval:[ 62/225] data_time 0.040645 (0.048608) train_time 0.814715 (0.807286)
#Eval:[ 63/225] data_time 0.040831 (0.048487) train_time 0.811918 (0.807359)
#Eval:[ 64/225] data_time 0.040498 (0.048364) train_time 0.811884 (0.807428)
#Eval:[ 65/225] data_time 0.039673 (0.048232) train_time 0.814446 (0.807535)
#Eval:[ 66/225] data_time 0.040010 (0.048110) train_time 0.816979 (0.807676)
#Eval:[ 67/225] data_time 0.040763 (0.048001) train_time 0.815673 (0.807793)
#Eval:[ 68/225] data_time 0.040116 (0.047887) train_time 0.815871 (0.807910)
#Eval:[ 69/225] data_time 0.040113 (0.047776) train_time 0.812022 (0.807969)
#Eval:[ 70/225] data_time 0.042265 (0.047699) train_time 0.819192 (0.808127)
#Eval:[ 71/225] data_time 0.040488 (0.047598) train_time 0.802501 (0.808049)
#Eval:[ 72/225] data_time 0.041070 (0.047509) train_time 0.805149 (0.808009)
#Eval:[ 73/225] data_time 0.042054 (0.047435) train_time 0.815068 (0.808105)
#Eval:[ 74/225] data_time 0.040750 (0.047346) train_time 0.809044 (0.808117)
#Eval:[ 75/225] data_time 0.040011 (0.047250) train_time 0.813235 (0.808184)
#Eval:[ 76/225] data_time 0.043043 (0.047195) train_time 0.811157 (0.808223)
#Eval:[ 77/225] data_time 0.039876 (0.047101) train_time 0.813111 (0.808286)
#Eval:[ 78/225] data_time 0.040135 (0.047013) train_time 0.810924 (0.808319)
#Eval:[ 79/225] data_time 0.040306 (0.046929) train_time 0.812062 (0.808366)
#Eval:[ 80/225] data_time 0.040752 (0.046853) train_time 0.809658 (0.808382)
#Eval:[ 81/225] data_time 0.040653 (0.046777) train_time 0.816320 (0.808479)
#Eval:[ 82/225] data_time 0.040388 (0.046700) train_time 0.810328 (0.808501)
#Eval:[ 83/225] data_time 0.040740 (0.046629) train_time 0.816155 (0.808592)
#Eval:[ 84/225] data_time 0.041280 (0.046566) train_time 0.813080 (0.808645)
#Eval:[ 85/225] data_time 0.040848 (0.046500) train_time 0.813959 (0.808707)
#Eval:[ 86/225] data_time 0.040094 (0.046426) train_time 0.814204 (0.808770)
#Eval:[ 87/225] data_time 0.040827 (0.046363) train_time 0.809299 (0.808776)
#Eval:[ 88/225] data_time 0.039530 (0.046286) train_time 0.811571 (0.808807)
#Eval:[ 89/225] data_time 0.040482 (0.046221) train_time 0.806065 (0.808777)
#Eval:[ 90/225] data_time 0.040568 (0.046159) train_time 0.813799 (0.808832)
#Eval:[ 91/225] data_time 0.041428 (0.046108) train_time 0.812696 (0.808874)
#Eval:[ 92/225] data_time 0.040262 (0.046045) train_time 0.807937 (0.808864)
#Eval:[ 93/225] data_time 0.041116 (0.045993) train_time 0.808364 (0.808859)
#Eval:[ 94/225] data_time 0.040158 (0.045931) train_time 0.811798 (0.808890)
#Eval:[ 95/225] data_time 0.040652 (0.045876) train_time 0.807996 (0.808880)
#Eval:[ 96/225] data_time 0.040504 (0.045821) train_time 0.819683 (0.808992)
#Eval:[ 97/225] data_time 0.040604 (0.045767) train_time 0.810562 (0.809008)
#Eval:[ 98/225] data_time 0.040298 (0.045712) train_time 0.818260 (0.809101)
#Eval:[ 99/225] data_time 0.040197 (0.045657) train_time 0.813555 (0.809146)
#Eval:[100/225] data_time 0.042036 (0.045621) train_time 0.820814 (0.809261)
#Eval:[101/225] data_time 0.042076 (0.045586) train_time 0.820296 (0.809369)
#Eval:[102/225] data_time 0.042270 (0.045554) train_time 0.819977 (0.809472)
#Eval:[103/225] data_time 0.040020 (0.045501) train_time 0.821351 (0.809587)
#Eval:[104/225] data_time 0.040334 (0.045452) train_time 0.814307 (0.809631)
#Eval:[105/225] data_time 0.041071 (0.045411) train_time 0.819901 (0.809728)
#Eval:[106/225] data_time 0.040657 (0.045366) train_time 0.816109 (0.809788)
#Eval:[107/225] data_time 0.041048 (0.045326) train_time 0.819442 (0.809877)
#Eval:[108/225] data_time 0.041171 (0.045288) train_time 0.816974 (0.809942)
#Eval:[109/225] data_time 0.040030 (0.045240) train_time 0.816332 (0.810001)
#Eval:[110/225] data_time 0.040808 (0.045200) train_time 0.812515 (0.810023)
#Eval:[111/225] data_time 0.040519 (0.045158) train_time 0.816895 (0.810085)
#Eval:[112/225] data_time 0.041322 (0.045125) train_time 0.816286 (0.810139)
#Eval:[113/225] data_time 0.040582 (0.045085) train_time 0.814588 (0.810178)
#Eval:[114/225] data_time 0.042142 (0.045059) train_time 0.820069 (0.810264)
#Eval:[115/225] data_time 0.041483 (0.045028) train_time 0.814595 (0.810302)
#Eval:[116/225] data_time 0.041713 (0.045000) train_time 0.820677 (0.810390)
#Eval:[117/225] data_time 0.041497 (0.044970) train_time 0.815148 (0.810431)
#Eval:[118/225] data_time 0.039872 (0.044927) train_time 0.818884 (0.810502)
#Eval:[119/225] data_time 0.040807 (0.044893) train_time 0.814259 (0.810533)
#Eval:[120/225] data_time 0.042302 (0.044872) train_time 0.820152 (0.810613)
#Eval:[121/225] data_time 0.040751 (0.044838) train_time 0.815587 (0.810653)
#Eval:[122/225] data_time 0.041031 (0.044807) train_time 0.822116 (0.810747)
#Eval:[123/225] data_time 0.040605 (0.044773) train_time 0.816167 (0.810790)
#Eval:[124/225] data_time 0.040553 (0.044739) train_time 0.821086 (0.810873)
#Eval:[125/225] data_time 0.040888 (0.044709) train_time 0.819381 (0.810940)
#Eval:[126/225] data_time 0.041299 (0.044682) train_time 0.818301 (0.810998)
#Eval:[127/225] data_time 0.042050 (0.044661) train_time 0.821964 (0.811084)
#Eval:[128/225] data_time 0.040050 (0.044626) train_time 0.819672 (0.811150)
#Eval:[129/225] data_time 0.040637 (0.044595) train_time 0.821504 (0.811230)
#Eval:[130/225] data_time 0.041214 (0.044569) train_time 0.821934 (0.811312)
#Eval:[131/225] data_time 0.040955 (0.044542) train_time 0.823735 (0.811406)
#Eval:[132/225] data_time 0.042319 (0.044525) train_time 0.819385 (0.811466)
#Eval:[133/225] data_time 0.040641 (0.044496) train_time 0.821653 (0.811542)
#Eval:[134/225] data_time 0.041009 (0.044470) train_time 0.816224 (0.811577)
#Eval:[135/225] data_time 0.040229 (0.044439) train_time 0.822478 (0.811657)
#Eval:[136/225] data_time 0.041022 (0.044414) train_time 0.823263 (0.811741)
#Eval:[137/225] data_time 0.041965 (0.044396) train_time 0.822629 (0.811820)
#Eval:[138/225] data_time 0.041355 (0.044374) train_time 0.819581 (0.811876)
#Eval:[139/225] data_time 0.040809 (0.044349) train_time 0.813878 (0.811891)
#Eval:[140/225] data_time 0.040011 (0.044318) train_time 0.819565 (0.811945)
#Eval:[141/225] data_time 0.040848 (0.044294) train_time 0.813883 (0.811959)
#Eval:[142/225] data_time 0.041620 (0.044275) train_time 0.819506 (0.812011)
#Eval:[143/225] data_time 0.041525 (0.044256) train_time 0.815936 (0.812039)
#Eval:[144/225] data_time 0.044354 (0.044257) train_time 0.818827 (0.812085)
#Eval:[145/225] data_time 0.041060 (0.044235) train_time 0.821224 (0.812148)
#Eval:[146/225] data_time 0.041163 (0.044214) train_time 0.814263 (0.812162)
#Eval:[147/225] data_time 0.048307 (0.044241) train_time 0.823898 (0.812242)
#Eval:[148/225] data_time 0.041201 (0.044221) train_time 0.816626 (0.812271)
#Eval:[149/225] data_time 0.040734 (0.044198) train_time 0.818538 (0.812313)
#Eval:[150/225] data_time 0.040458 (0.044173) train_time 0.820384 (0.812366)
#Eval:[151/225] data_time 0.040171 (0.044147) train_time 0.823809 (0.812442)
#Eval:[152/225] data_time 0.041587 (0.044130) train_time 0.826429 (0.812533)
#Eval:[153/225] data_time 0.040336 (0.044105) train_time 0.815126 (0.812550)
#Eval:[154/225] data_time 0.041076 (0.044086) train_time 0.820828 (0.812603)
#Eval:[155/225] data_time 0.040574 (0.044063) train_time 0.822982 (0.812670)
#Eval:[156/225] data_time 0.043104 (0.044057) train_time 0.823233 (0.812737)
#Eval:[157/225] data_time 0.041285 (0.044040) train_time 0.826391 (0.812824)
#Eval:[158/225] data_time 0.040637 (0.044018) train_time 0.816491 (0.812847)
#Eval:[159/225] data_time 0.040037 (0.043993) train_time 0.820456 (0.812894)
#Eval:[160/225] data_time 0.040802 (0.043974) train_time 0.817626 (0.812924)
#Eval:[161/225] data_time 0.039881 (0.043948) train_time 0.819187 (0.812962)
#Eval:[162/225] data_time 0.041099 (0.043931) train_time 0.819306 (0.813001)
#Eval:[163/225] data_time 0.041152 (0.043914) train_time 0.819688 (0.813042)
#Eval:[164/225] data_time 0.040649 (0.043894) train_time 0.824448 (0.813111)
#Eval:[165/225] data_time 0.041859 (0.043882) train_time 0.820320 (0.813154)
#Eval:[166/225] data_time 0.040072 (0.043859) train_time 0.818843 (0.813189)
#Eval:[167/225] data_time 0.040809 (0.043841) train_time 0.815692 (0.813203)
#Eval:[168/225] data_time 0.040725 (0.043822) train_time 0.822592 (0.813259)
#Eval:[169/225] data_time 0.041077 (0.043806) train_time 0.820768 (0.813303)
#Eval:[170/225] data_time 0.040932 (0.043789) train_time 0.822658 (0.813358)
#Eval:[171/225] data_time 0.040974 (0.043773) train_time 0.823002 (0.813414)
#Eval:[172/225] data_time 0.041114 (0.043758) train_time 0.817184 (0.813436)
#Eval:[173/225] data_time 0.040571 (0.043739) train_time 0.826567 (0.813511)
#Eval:[174/225] data_time 0.040970 (0.043724) train_time 0.817444 (0.813534)
#Eval:[175/225] data_time 0.040405 (0.043705) train_time 0.821823 (0.813581)
#Eval:[176/225] data_time 0.041468 (0.043692) train_time 0.821515 (0.813626)
#Eval:[177/225] data_time 0.040689 (0.043675) train_time 0.829367 (0.813714)
#Eval:[178/225] data_time 0.043226 (0.043673) train_time 0.822716 (0.813764)
#Eval:[179/225] data_time 0.040493 (0.043655) train_time 0.814341 (0.813768)
#Eval:[180/225] data_time 0.040918 (0.043640) train_time 0.819122 (0.813797)
#Eval:[181/225] data_time 0.040753 (0.043624) train_time 0.815603 (0.813807)
#Eval:[182/225] data_time 0.048748 (0.043652) train_time 0.827286 (0.813881)
#Eval:[183/225] data_time 0.040855 (0.043637) train_time 0.820357 (0.813916)
#Eval:[184/225] data_time 0.041434 (0.043625) train_time 0.813671 (0.813915)
#Eval:[185/225] data_time 0.041054 (0.043611) train_time 0.822764 (0.813962)
#Eval:[186/225] data_time 0.040511 (0.043595) train_time 0.815666 (0.813971)
#Eval:[187/225] data_time 0.040392 (0.043577) train_time 0.820901 (0.814008)
#Eval:[188/225] data_time 0.044682 (0.043583) train_time 0.825225 (0.814067)
#Eval:[189/225] data_time 0.040749 (0.043568) train_time 0.821012 (0.814104)
#Eval:[190/225] data_time 0.040810 (0.043554) train_time 0.821078 (0.814141)
#Eval:[191/225] data_time 0.041850 (0.043545) train_time 0.821648 (0.814180)
#Eval:[192/225] data_time 0.039746 (0.043525) train_time 0.820654 (0.814213)
#Eval:[193/225] data_time 0.040885 (0.043512) train_time 0.817120 (0.814228)
#Eval:[194/225] data_time 0.041700 (0.043503) train_time 0.822229 (0.814269)
#Eval:[195/225] data_time 0.041192 (0.043491) train_time 0.824572 (0.814322)
#Eval:[196/225] data_time 0.040723 (0.043477) train_time 0.821064 (0.814356)
#Eval:[197/225] data_time 0.040633 (0.043462) train_time 0.815858 (0.814364)
#Eval:[198/225] data_time 0.041276 (0.043451) train_time 0.821459 (0.814399)
#Eval:[199/225] data_time 0.041371 (0.043441) train_time 0.820885 (0.814432)
#Eval:[200/225] data_time 0.040414 (0.043426) train_time 0.821969 (0.814469)
#Eval:[201/225] data_time 0.039814 (0.043408) train_time 0.815174 (0.814473)
#Eval:[202/225] data_time 0.039946 (0.043391) train_time 0.817539 (0.814488)
#Eval:[203/225] data_time 0.040758 (0.043378) train_time 0.820333 (0.814516)
#Eval:[204/225] data_time 0.042162 (0.043372) train_time 0.815993 (0.814524)
#Eval:[205/225] data_time 0.039959 (0.043356) train_time 0.819163 (0.814546)
#Eval:[206/225] data_time 0.040344 (0.043341) train_time 0.813791 (0.814542)
#Eval:[207/225] data_time 0.040740 (0.043328) train_time 0.822119 (0.814579)
#Eval:[208/225] data_time 0.040993 (0.043317) train_time 0.819627 (0.814603)
#Eval:[209/225] data_time 0.041491 (0.043309) train_time 0.817587 (0.814617)
#Eval:[210/225] data_time 0.041445 (0.043300) train_time 0.823525 (0.814659)
#Eval:[211/225] data_time 0.040802 (0.043288) train_time 0.814985 (0.814661)
#Eval:[212/225] data_time 0.040326 (0.043274) train_time 0.817389 (0.814674)
#Eval:[213/225] data_time 0.040569 (0.043261) train_time 0.815536 (0.814678)
#Eval:[214/225] data_time 0.040926 (0.043251) train_time 0.821394 (0.814709)
#Eval:[215/225] data_time 0.040218 (0.043237) train_time 0.817742 (0.814723)
#Eval:[216/225] data_time 0.040501 (0.043224) train_time 0.815880 (0.814728)
#Eval:[217/225] data_time 0.041519 (0.043216) train_time 0.821725 (0.814761)
#Eval:[218/225] data_time 0.042224 (0.043212) train_time 0.821911 (0.814793)
#Eval:[219/225] data_time 0.041394 (0.043203) train_time 0.816527 (0.814801)
#Eval:[220/225] data_time 0.040535 (0.043191) train_time 0.822128 (0.814834)
#Eval:[221/225] data_time 0.040533 (0.043179) train_time 0.816509 (0.814842)
#Eval:[222/225] data_time 0.040094 (0.043165) train_time 0.818780 (0.814859)
#Eval:[223/225] data_time 0.041802 (0.043159) train_time 0.818001 (0.814873)
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extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.9996381998062134
dmean : 0.014132329262793064
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09444835036993027
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:43 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 0.999423623085022
dmean : 0.0008302876376546919
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.021966466680169106
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:06:49 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling created
Origin: [0.0, 0.0, 0.0]
detected mode mapc 1, mapr 2, maps 3
information of /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/input.mrc
The recording mode in the mrc file:2
XYZ dim:271,271,271
location of first column/row/section in unit cell:0,0,0
sampling along X,Y,Z axis of unit cell:271,271,271
cell dimensions in angstroms:271.000000,271.000000,271.000000
Cell angles in degree:90,90,90
axis mode:(1,2,3)
density statistics:min(-2.006058),max(3.159605),mean(0.012243)
space group number:1
extended data:0
origin state:(0.000000,0.000000,0.000000)
density data shape:
(271, 271, 271)
min density:0.000000
max density:3.159605
number of voxels: 19902511
width of x,y,z:(1.000000,1.000000,1.000000)
order mode:1
useful points: 16288
in total chain useful percentage 0.000818
after normalizing pho dens min 0.0000 max 0.9997
useful points: 22051
in total chain useful percentage 0.001108
dens shape now
(271, 271, 271)
after normalizing sugar dens min 0.0000 max 0.9996
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/pho_LDP created
carry on mean shifting jobs
useful points 16288
set up filters
fmaxd=6.000000
mean shift 0 / 16288
mean shift 1000 / 16288
mean shift 2000 / 16288
mean shift 3000 / 16288
mean shift 4000 / 16288
mean shift 5000 / 16288
mean shift 6000 / 16288
mean shift 7000 / 16288
mean shift 8000 / 16288
mean shift 9000 / 16288
mean shift 10000 / 16288
mean shift 11000 / 16288
mean shift 12000 / 16288
mean shift 13000 / 16288
mean shift 14000 / 16288
mean shift 15000 / 16288
mean shift 16000 / 16288
finishing meanshifting with 16288 points
here we get the density range 9.485158
0
10000
merging finishing with 141 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.600675582885742
dmean : 5.57807506993413e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.021728407591581345
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:07:24 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 34 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_LDP created
carry on mean shifting jobs
useful points 22051
set up filters
fmaxd=6.000000
mean shift 0 / 22051
mean shift 1000 / 22051
mean shift 2000 / 22051
mean shift 3000 / 22051
mean shift 4000 / 22051
mean shift 5000 / 22051
mean shift 6000 / 22051
mean shift 7000 / 22051
mean shift 8000 / 22051
mean shift 9000 / 22051
mean shift 10000 / 22051
mean shift 11000 / 22051
mean shift 12000 / 22051
mean shift 13000 / 22051
mean shift 14000 / 22051
mean shift 15000 / 22051
mean shift 16000 / 22051
mean shift 17000 / 22051
mean shift 18000 / 22051
mean shift 19000 / 22051
mean shift 20000 / 22051
mean shift 21000 / 22051
mean shift 22000 / 22051
finishing meanshifting with 22051 points
here we get the density range 9.946610
0
10000
20000
merging finishing with 181 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.048613548278809
dmean : 7.974963955348358e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.027282539755105972
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:07:47 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 57 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_graph created
0
10000
20000
number of possible connected edges by differen ori data:313
skip edges with distance 14.777493
skip edges with distance 15.687752
skip edges with distance 13.441810
skip edges with distance 12.313532
skip edges with distance 11.735175
skip edges with distance 10.331086
skip edges with distance 10.178144
skip edges with distance 10.254010
skip edges with distance 11.361568
skip edges with distance 10.557541
skip edges with distance 10.159017
skip edges with distance 18.316433
skip edges with distance 14.009447
skip edges with distance 10.096806
skip edges with distance 11.412779
skip edges with distance 11.492459
skip edges with distance 11.367592
skip edges with distance 12.261071
skip edges with distance 10.064836
skip edges with distance 11.036328
skip edges with distance 11.381088
skip edges with distance 15.269321
sorting edge for MST preparataion 288
filtered edge numbers 313
297/313 edges are remained after prob map checking
filtered edge numbers 297
Further adding 240 edges based on extending and checking base region
filtered edge numbers 537
0
edge density min 1.00 max 200.78 mean 14.83
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search/sub_graph0 created
filtered edge numbers 537
number of edges in the data: 1025
distance mean 1548.454634
updated distance mean 46744.975788
number vehicles: 5 adj matrix shape: 182
drop penalty 42156
start routing
add capacity
add penalty
add params
Objective: 213867
Route for vehicle 0:
0 -> 15 -> 20 -> 12 -> 13 -> 8 -> 1 -> 10 -> 14 -> 22 -> 23 -> 25 -> 27 -> 32 -> 30 -> 28 -> 34 -> 37 -> 35 -> 38 -> 42 -> 41 -> 48 -> 47 -> 46 -> 54 -> 52 -> 55 -> 58 -> 57 -> 66 -> 63 -> 61 -> 62 -> 67 -> 71 -> 68 -> 72 -> 73 -> 74 -> 75 -> 78 -> 84 -> 83 -> 93 -> 91 -> 92 -> 97 -> 96 -> 102 -> 101 -> 106 -> 104 -> 110 -> 107 -> 109 -> 113 -> 114 -> 115 -> 116 -> 119 -> 122 -> 117 -> 118 -> 123 -> 124 -> 129 -> 132 -> 131 -> 143 -> 137 -> 138 -> 146 -> 148 -> 155 -> 152 -> 159 -> 162 -> 156 -> 166 -> 157 -> 158 -> 161 -> 163 -> 165 -> 164 -> 169 -> 171 -> 174 -> 172 -> 176 -> 181 -> 178 -> 180 -> 179 -> 177 -> 173 -> 175 -> 170 -> 167 -> 154 -> 153 -> 150 -> 151 -> 149 -> 147 -> 145 -> 144 -> 140 -> 136 -> 139 -> 135 -> 141 -> 142 -> 133 -> 134 -> 130 -> 127 -> 125 -> 126 -> 120 -> 121 -> 112 -> 111 -> 108 -> 105 -> 103 -> 99 -> 98 -> 100 -> 95 -> 94 -> 89 -> 88 -> 90 -> 85 -> 86 -> 87 -> 81 -> 82 -> 80 -> 77 -> 79 -> 76 -> 70 -> 69 -> 65 -> 60 -> 56 -> 53 -> 51 -> 50 -> 49 -> 44 -> 45 -> 43 -> 40 -> 39 -> 36 -> 33 -> 31 -> 29 -> 21 -> 24 -> 19 -> 18 -> 17 -> 11 -> 9 -> 3 -> 2 -> 7 -> 5 -> 6 -> 4 -> 0
Distance of the route: 165891m
Route for vehicle 1:
0 -> 64 -> 59 -> 0
Distance of the route: 20675m
Route for vehicle 2:
0 -> 128 -> 0
Distance of the route: 0m
Route for vehicle 3:
0 -> 26 -> 16 -> 0
Distance of the route: 20698m
Route for vehicle 4:
0 -> 160 -> 168 -> 0
Distance of the route: 6603m
Maximum of the route distances: 165891m
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/sugar_search/sub_graph0/Prune created
Extract search dict 174, GT search dict 181
search length 174, return search result length 174
filtered edge numbers 536
174 node path find 1 sub path
in total we collected 1 path candidates
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_LDP created
useful points: 2709
in total chain useful percentage 0.000136
after normalizing pho dens min 0.0000 max 0.9988
carry on mean shifting jobs
useful points 2709
set up filters
fmaxd=6.000000
mean shift 0 / 2709
mean shift 1000 / 2709
mean shift 2000 / 2709
finishing meanshifting with 2709 points
here we get the density range 9.808118
0
merging finishing with 33 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.931495666503906
dmean : 1.1405014447518624e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.009559660218656063
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:22 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 9 isolated grid points
useful points: 3178
in total chain useful percentage 0.000160
after normalizing pho dens min 0.0000 max 0.9996
carry on mean shifting jobs
useful points 3178
set up filters
fmaxd=6.000000
mean shift 0 / 3178
mean shift 1000 / 3178
mean shift 2000 / 3178
mean shift 3000 / 3178
finishing meanshifting with 3178 points
here we get the density range 9.771262
0
merging finishing with 33 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.886703491210938
dmean : 1.1659149095066823e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.009832863695919514
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:29 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 13 isolated grid points
useful points: 2960
in total chain useful percentage 0.000149
after normalizing pho dens min 0.0000 max 0.9993
carry on mean shifting jobs
useful points 2960
set up filters
fmaxd=6.000000
mean shift 0 / 2960
mean shift 1000 / 2960
mean shift 2000 / 2960
finishing meanshifting with 2960 points
here we get the density range 9.877241
0
merging finishing with 34 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 9.980541229248047
dmean : 8.555003660148941e-06
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.00806853361427784
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:37 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 56 isolated grid points
useful points: 5616
in total chain useful percentage 0.000282
after normalizing pho dens min 0.0000 max 0.9998
carry on mean shifting jobs
useful points 5616
set up filters
fmaxd=6.000000
mean shift 0 / 5616
mean shift 1000 / 5616
mean shift 2000 / 5616
mean shift 3000 / 5616
mean shift 4000 / 5616
mean shift 5000 / 5616
finishing meanshifting with 5616 points
here we get the density range 9.979040
0
merging finishing with 52 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.098882675170898
dmean : 1.816607800719794e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.012404625304043293
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:46 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 27 isolated grid points
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_LDP existed
useful points: 13816
in total chain useful percentage 0.000694
after normalizing pho dens min 0.0000 max 0.9994
carry on mean shifting jobs
useful points 13816
set up filters
fmaxd=6.000000
mean shift 0 / 13816
mean shift 1000 / 13816
mean shift 2000 / 13816
mean shift 3000 / 13816
mean shift 4000 / 13816
mean shift 5000 / 13816
mean shift 6000 / 13816
mean shift 7000 / 13816
mean shift 8000 / 13816
mean shift 9000 / 13816
mean shift 10000 / 13816
mean shift 11000 / 13816
mean shift 12000 / 13816
mean shift 13000 / 13816
finishing meanshifting with 13816 points
here we get the density range 6.504001
0
10000
merging finishing with 116 left
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
Starting phenix.real_space_refine (version: 1.20)
on Fri Jun 9 14:19:52 2023 by webdklab
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb
Found real_map, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
resolution=3.7000
output.suffix=_phenix_refine
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
default_real_map = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
model {
file = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb"
}
default_model = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Final_Assemble_geo_formated.pdb"
}
resolution = 3.7000
output {
suffix = _phenix_refine
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.038
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.00s
Monomer Library directory:
"/apps/phenix/phenix-1.20-4459/modules/chem_data/mon_lib"
Total number of atoms: 2132
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2132
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 97, 2132
Inner-chain residues flagged as termini: ['pdbres=" G A 2 "', 'pdbres=" G A 3 "', 'pdbres=" U A 4 "', 'pdbres=" U A 5 "', 'pdbres=" U A 6 "', 'pdbres=" G A 7 "', 'pdbres=" G A 8 "', 'pdbres=" G A 9 "', 'pdbres=" A A 10 "', 'pdbres=" U A 11 "', 'pdbres=" A A 12 "', 'pdbres=" C A 13 "', 'pdbres=" C A 14 "', 'pdbres=" U A 15 "', 'pdbres=" G A 16 "', 'pdbres=" U A 17 "', 'pdbres=" U A 18 "', 'pdbres=" C A 19 "', 'pdbres=" C A 20 "', 'pdbres=" C A 21 "', 'pdbres=" C A 22 "', 'pdbres=" C A 23 "', 'pdbres=" U A 24 "', 'pdbres=" U A 25 "', 'pdbres=" U A 26 "', 'pdbres=" A A 27 "', 'pdbres=" C A 28 "', 'pdbres=" A A 29 "', 'pdbres=" A A 30 "', 'pdbres=" G A 31 "', 'pdbres=" C A 32 "', 'pdbres=" C A 33 "', 'pdbres=" A A 34 "', 'pdbres=" C A 35 "', 'pdbres=" G A 36 "', 'pdbres=" G A 37 "', 'pdbres=" G A 38 "', 'pdbres=" U A 39 "', 'pdbres=" U A 40 "', 'pdbres=" A A 41 "', 'pdbres=" U A 42 "', 'pdbres=" U A 43 "', 'pdbres=" G A 44 "', 'pdbres=" U A 45 "', 'pdbres=" U A 46 "', 'pdbres=" G A 47 "', 'pdbres=" G A 48 "', 'pdbres=" G A 49 "', 'pdbres=" U A 50 "', 'pdbres=" U A 51 "', 'pdbres=" G A 52 "', 'pdbres=" C A 53 "', 'pdbres=" C A 54 "', 'pdbres=" C A 55 "', 'pdbres=" C A 56 "', 'pdbres=" C A 57 "', 'pdbres=" C A 58 "', 'pdbres=" C A 59 "', 'pdbres=" C A 60 "', 'pdbres=" C A 61 "', 'pdbres=" A A 62 "', 'pdbres=" U A 63 "', 'pdbres=" C A 64 "', 'pdbres=" U A 65 "', 'pdbres=" U A 66 "', 'pdbres=" U A 67 "', 'pdbres=" A A 68 "', 'pdbres=" C A 69 "', 'pdbres=" U A 70 "', 'pdbres=" U A 71 "', 'pdbres=" G A 72 "', 'pdbres=" G A 73 "', 'pdbres=" C A 74 "', 'pdbres=" U A 75 "', 'pdbres=" C A 76 "', 'pdbres=" C A 77 "', 'pdbres=" C A 78 "', 'pdbres=" U A 79 "', 'pdbres=" U A 80 "', 'pdbres=" A A 81 "', 'pdbres=" A A 82 "', 'pdbres=" G A 83 "', 'pdbres=" U A 84 "', 'pdbres=" G A 85 "', 'pdbres=" U A 86 "', 'pdbres=" U A 87 "', 'pdbres=" A A 88 "', 'pdbres=" C A 89 "', 'pdbres=" A A 90 "', 'pdbres=" G A 91 "', 'pdbres=" G A 92 "', 'pdbres=" G A 93 "', 'pdbres=" C A 94 "', 'pdbres=" C A 95 "', 'pdbres=" U A 96 "']
Classifications: {'RNA': 97}
Modifications used: {'rna2p_pur': 36, 'p5*END': 97, 'rna2p_pyr': 61}
Link IDs: {'rna2p': 96}
Chain breaks: 20
Time building chain proxies: 0.62, per 1000 atoms: 0.29
Number of scatterers: 2132
At special positions: 0
Unit cell: (49, 59, 138, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
P 97 15.00
O 794 8.00
N 332 7.00
C 909 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.98
Conformation dependent library (CDL) restraints added in 5.4 milliseconds
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 0
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 0 sheets defined
0.0% alpha, 0.0% beta
11 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.24
Creating SS restraints...
No hydrogen bonds defined for protein.
Restraints generated for nucleic acids:
22 hydrogen bonds
20 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 0.16
Time building geometry restraints manager: 0.80 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.25 - 0.80: 40
0.80 - 1.34: 325
1.34 - 1.89: 1955
1.89 - 2.44: 9
2.44 - 2.98: 12
Warning: very small bond lengths.
Bond restraints: 2341
Sorted by residual:
bond pdb="O3' C A 61 "
pdb="P A A 62 "
ideal model delta sigma weight residual
1.607 2.984 -1.377 1.50e-02 4.44e+03 8.43e+03
bond pdb="O3' A A 62 "
pdb="P U A 63 "
ideal model delta sigma weight residual
1.607 2.978 -1.371 1.50e-02 4.44e+03 8.35e+03
bond pdb="O3' G A 8 "
pdb="P G A 9 "
ideal model delta sigma weight residual
1.607 0.249 1.358 1.50e-02 4.44e+03 8.20e+03
bond pdb="O3' G A 16 "
pdb="P U A 17 "
ideal model delta sigma weight residual
1.607 2.958 -1.351 1.50e-02 4.44e+03 8.12e+03
bond pdb="O3' A A 30 "
pdb="P G A 31 "
ideal model delta sigma weight residual
1.607 0.256 1.351 1.50e-02 4.44e+03 8.11e+03
... (remaining 2336 not shown)
Histogram of bond angle deviations from ideal:
2.96 - 33.68: 30
33.68 - 64.39: 63
64.39 - 95.11: 96
95.11 - 125.82: 3368
125.82 - 156.53: 174
Bond angle restraints: 3731
Sorted by residual:
angle pdb="C3' C A 23 "
pdb="O3' C A 23 "
pdb="P U A 24 "
ideal model delta sigma weight residual
120.20 15.25 104.95 1.50e+00 4.44e-01 4.90e+03
angle pdb="C3' U A 17 "
pdb="O3' U A 17 "
pdb="P U A 18 "
ideal model delta sigma weight residual
120.20 15.49 104.71 1.50e+00 4.44e-01 4.87e+03
angle pdb="C3' C A 33 "
pdb="O3' C A 33 "
pdb="P A A 34 "
ideal model delta sigma weight residual
120.20 16.30 103.90 1.50e+00 4.44e-01 4.80e+03
angle pdb="C3' C A 89 "
pdb="O3' C A 89 "
pdb="P A A 90 "
ideal model delta sigma weight residual
120.20 18.72 101.48 1.50e+00 4.44e-01 4.58e+03
angle pdb="C3' U A 26 "
pdb="O3' U A 26 "
pdb="P A A 27 "
ideal model delta sigma weight residual
120.20 19.91 100.29 1.50e+00 4.44e-01 4.47e+03
... (remaining 3726 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 32.33: 423
32.33 - 64.66: 447
64.66 - 96.98: 101
96.98 - 129.31: 101
129.31 - 161.64: 29
Dihedral angle restraints: 1101
sinusoidal: 1101
harmonic: 0
Sorted by residual:
dihedral pdb="C5' G A 49 "
pdb="C4' G A 49 "
pdb="C3' G A 49 "
pdb="O3' G A 49 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.20 -114.80 1 8.00e+00 1.56e-02 2.13e+02
dihedral pdb="C5' G A 38 "
pdb="C4' G A 38 "
pdb="C3' G A 38 "
pdb="O3' G A 38 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.20 -114.80 1 8.00e+00 1.56e-02 2.13e+02
dihedral pdb="C5' G A 16 "
pdb="C4' G A 16 "
pdb="C3' G A 16 "
pdb="O3' G A 16 "
ideal model delta sinusoidal sigma weight residual
147.00 -98.21 -114.79 1 8.00e+00 1.56e-02 2.13e+02
... (remaining 1098 not shown)
Histogram of chiral volume deviations from ideal:
0.533 - 1.519: 97
1.519 - 2.506: 0
2.506 - 3.493: 0
3.493 - 4.480: 0
4.480 - 5.466: 388
Chirality restraints: 485
Sorted by residual:
chirality pdb="C3' G A 9 "
pdb="C4' G A 9 "
pdb="O3' G A 9 "
pdb="C2' G A 9 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
chirality pdb="C3' C A 64 "
pdb="C4' C A 64 "
pdb="O3' C A 64 "
pdb="C2' C A 64 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
chirality pdb="C3' C A 20 "
pdb="C4' C A 20 "
pdb="O3' C A 20 "
pdb="C2' C A 20 "
both_signs ideal model delta sigma weight residual
False -2.74 2.72 -5.47 2.00e-01 2.50e+01 7.47e+02
... (remaining 482 not shown)
Planarity restraints: 97
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb="C1' G A 73 " -0.000 2.00e-02 2.50e+03 1.93e-03 1.11e-01
pdb="N9 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="C8 G A 73 " -0.001 2.00e-02 2.50e+03
pdb="N7 G A 73 " 0.000 2.00e-02 2.50e+03
pdb="C5 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="C6 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="O6 G A 73 " 0.002 2.00e-02 2.50e+03
pdb="N1 G A 73 " -0.006 2.00e-02 2.50e+03
pdb="C2 G A 73 " 0.001 2.00e-02 2.50e+03
pdb="N2 G A 73 " 0.002 2.00e-02 2.50e+03
pdb="N3 G A 73 " 0.000 2.00e-02 2.50e+03
pdb="C4 G A 73 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' G A 83 " 0.000 2.00e-02 2.50e+03 1.92e-03 1.11e-01
pdb="N9 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C8 G A 83 " 0.000 2.00e-02 2.50e+03
pdb="N7 G A 83 " 0.001 2.00e-02 2.50e+03
pdb="C5 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C6 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="O6 G A 83 " -0.002 2.00e-02 2.50e+03
pdb="N1 G A 83 " 0.006 2.00e-02 2.50e+03
pdb="C2 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="N2 G A 83 " -0.001 2.00e-02 2.50e+03
pdb="N3 G A 83 " -0.000 2.00e-02 2.50e+03
pdb="C4 G A 83 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' G A 3 " -0.000 2.00e-02 2.50e+03 1.90e-03 1.09e-01
pdb="N9 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C8 G A 3 " -0.001 2.00e-02 2.50e+03
pdb="N7 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C5 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C6 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="O6 G A 3 " 0.002 2.00e-02 2.50e+03
pdb="N1 G A 3 " -0.006 2.00e-02 2.50e+03
pdb="C2 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="N2 G A 3 " 0.002 2.00e-02 2.50e+03
pdb="N3 G A 3 " 0.000 2.00e-02 2.50e+03
pdb="C4 G A 3 " -0.000 2.00e-02 2.50e+03
... (remaining 94 not shown)
Histogram of nonbonded interaction distances:
0.15 - 1.10: 253
1.10 - 2.05: 1451
2.05 - 3.00: 4387
3.00 - 3.95: 8441
3.95 - 4.90: 11326
Warning: very small nonbonded interaction distances.
Nonbonded interactions: 25858
Sorted by model distance:
nonbonded pdb="O2 U A 11 "
pdb="C4' A A 12 "
model vdw
0.149 3.470
nonbonded pdb="O2' U A 96 "
pdb="OP2 C A 97 "
model vdw
0.243 2.440
nonbonded pdb="O2' C A 54 "
pdb="C1' C A 55 "
model vdw
0.316 3.470
nonbonded pdb="P G A 3 "
pdb="O3' G A 7 "
model vdw
0.322 3.400
nonbonded pdb="O2' A A 10 "
pdb="OP1 U A 11 "
model vdw
0.334 2.440
... (remaining 25853 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
P 97 5.49 5
C 909 2.51 5
N 332 2.21 5
O 794 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 5
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Write .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.530
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 1.020
Check model and map are aligned: 0.000
Convert atoms to be neutral: 0.050
Process input model: 3.850
Find NCS groups from input model: 0.010
Set up NCS constraints: 0.000
Set refine NCS operators: 0.000
Set scattering table: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:0.810
Set ADP refinement strategy: 0.000
Write .geo file: 1.260
Internal consistency checks: 0.000
Total: 7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2593
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.186 1.377 2341 Z=11.123
Angle : 13.450 105.036 3731 Z= 7.571
Chirality : 4.688 5.466 485
Planarity : 0.002 0.002 97
Dihedral : 58.071 161.640 1101
Min Nonbonded Distance : 0.149
Molprobity Statistics.
All-atom Clashscore : 206.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0185
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0068
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.9980
chunk 2 optimal weight: 0.9980
chunk 3 optimal weight: 0.9990
chunk 4 optimal weight: 0.9980
chunk 5 optimal weight: 1.9990
chunk 6 optimal weight: 0.8980
chunk 7 optimal weight: 0.7980
chunk 8 optimal weight: 0.6980
overall best weight: 0.8480
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2712
moved from start: 1.9161
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.037 0.623 2341 Z= 1.897
Angle : 6.445 65.919 3731 Z= 2.425
Chirality : 0.394 3.773 485
Planarity : 0.014 0.050 97
Dihedral : 42.046 176.109 1101
Min Nonbonded Distance : 1.664
Molprobity Statistics.
All-atom Clashscore : 78.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.025
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0288
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.019
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0072
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 5.9990
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 0.9980
chunk 3 optimal weight: 0.5980
chunk 4 optimal weight: 2.9990
chunk 5 optimal weight: 4.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.0483
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3790
moved from start: 2.4979
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.603 2341 Z= 1.810
Angle : 5.835 51.003 3731 Z= 2.141
Chirality : 0.375 3.699 485
Planarity : 0.009 0.042 97
Dihedral : 35.827 178.320 1101
Min Nonbonded Distance : 1.673
Molprobity Statistics.
All-atom Clashscore : 70.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.025
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0199
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0067
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 1.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 7.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 0.9980
overall best weight: 1.4988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4681
moved from start: 2.6838
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.600 2341 Z= 1.796
Angle : 5.803 50.069 3731 Z= 2.104
Chirality : 0.345 3.697 485
Planarity : 0.008 0.040 97
Dihedral : 34.571 163.364 1101
Min Nonbonded Distance : 1.674
Molprobity Statistics.
All-atom Clashscore : 81.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.036
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0288
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.017
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 7.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7490
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5132
moved from start: 2.9035
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.602 2341 Z= 1.806
Angle : 5.795 50.423 3731 Z= 2.094
Chirality : 0.345 3.699 485
Planarity : 0.008 0.042 97
Dihedral : 34.334 169.496 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 92.40
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.015
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0190
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0068
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 0.8980
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 9.9990
chunk 6 optimal weight: 1.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.116062 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.105365 restraints weight = 14392.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.106936 restraints weight = 6649.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.107952 restraints weight = 4363.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start: 2.9877
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.598 2341 Z= 1.796
Angle : 5.766 50.227 3731 Z= 2.078
Chirality : 0.347 3.682 485
Planarity : 0.008 0.042 97
Dihedral : 34.038 179.879 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 87.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
===============================================================================
Job complete
usr+sys time: 189.89 seconds
wall clock time: 5 minutes 22.26 seconds (322.26 seconds total)
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /apps/ccp4/ccp4-8.0/lib/data/monomers/
There are 249 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ALA.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ASP.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ASN.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/CYS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLN.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLY.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GLU.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PHE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/h/HIS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/i/ILE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/l/LYS.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/l/LEU.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/m/MET.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/m/MSE.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PRO.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/ARG.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/s/SER.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/THR.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/v/VAL.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/TRP.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/t/TYR.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/p/PO4.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/s/SO4.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/GOL.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/CIT.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/e/EDO.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/a/A.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/c/C.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/g/G.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/u/U.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DA.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DC.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DG.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/d/DT.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/h/HOH.cif
There are 2 data in /apps/ccp4/ccp4-8.0/lib/data/monomers/n/NA.cif
Spacegroup: P 1
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
INFO:: coot.py imported
Running python script /net/apps-server/ccp4/ccp4-8.0/coot_py2/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Kihara, Welcome to Coot version 0.9.8.7
[1m(set-display-intro-string "Good Afternoon Kihara, Welcome to Coot version 0.9.8.7")[0m
[1m(use-graphics-interface-state)[0m
INFO:: preferences directory /bio/dragon/webdklab/.coot-preferences does not exist. Won't read preferences.
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
[1m(use-graphics-interface-state)[0m
Good afternoon Kihara Lab Web User,UMS. Welcome to Coot 0.9.8.7.
[1m(set-display-intro-string "Good afternoon Kihara. Welcome to Coot 0.9.8.7")[0m
[1m(set-display-lists-for-maps 1)[0m
INFO:: preferences directory /bio/dragon/webdklab/.coot-preferences does not exist. Won't read .scm preferences.
[1m(filter-fileselection-filenames-state)[0m
[1m(get-active-map-drag-flag)[0m
INFO:: There are 1 command line scripts to run
coot_refine.py
calling run_script() for file coot_refine.py
debug:: run_script() on coot_refine.py
Running python script coot_refine.py
[1m(handle-read-draw-molecule-with-recentre "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb" 1)[0m
INFO:: Reading coordinate file: /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb
INFO:: file /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle1.pdb has been read.
Spacegroup: P 1
INFO:: Found 1 models
Model 1 had 0 links
debug:: g.safe_scheme_command() with command post-set-rotation-centre-hook
debug:: g.safe_scheme_command() with command post-read-model-hook
INFO:: in run_post_read_model_hook() pFunc 0xed2b40 is not callable
INFO:: in run_post_read_model_hook() pDict 0x7f92bd155168
INFO:: in run_post_read_model_hook() pModule 0x7f92bd141be8
Molecule 0 read successfully
INFO:: map file type was determined to be CCP4 type
DEBUG:: init xmap with P 1 Cell ( 271, 271, 271, 90, 90, 90) Nuvw = ( 271, 271, 271)
INFO:: map read 519 milliseconds
0.0789901 19871549 ****************************************************************************************************|
0.23697 542
0.394951 6095
0.552931 5823
0.710911 4535
0.868891 3427
1.02687 2888
1.18485 2311
1.34283 1788
1.50081 1260
1.65879 854
1.81677 571
1.97475 378
2.13273 215
2.29071 122
2.44869 90
2.60667 40
2.76465 11
2.92263 7
3.08062 4
3.2386 1
Pre-filter Map statistics: mean: 0.00131928 st.d: 0.0376485
Pre-filter Map statistics: min: 0 max: 3.15961
INFO:: n grid points: 19902511
INFO:: mean before filtering: 0.00131928
INFO:: variance before filtering: 0.00141741
INFO:: filter by ignoring 19871549 of 19902511 counts ( = 99.84%) with values around 0.000158 bounds 0 0.000316 from bin-number 0 of 10000
Post-filter Map statistics: mean: 0.848 st.d: 0.4394
Post-filter Map statistics: min: 0 max: 3.16
INFO:: map_density_distribution() took 179 milliseconds
------------------------- em 1 contour_level 1.977
Map extents: ..... 271 271 271
Map mean: ........ 0.848
Map rmsd: ........ 0.4394
Map maximum: ..... 3.16
Map minimum: ..... 0
[1m(set-contour-level-absolute 0.30)[0m
[1m(n-chains 0)[0m
[1m(chain_id 0 0)[0m
[1m(chain-n-residues "A" 0)[0m
There are 97 residues in chain A
[1m(resname-from-serial-number 0 "A" 0)[0m
[1m(seqnum-from-serial-number 0 "A" 0)[0m
[1m(insertion-code-from-serial-number 0 "A" 0)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 1)[0m
[1m(seqnum-from-serial-number 0 "A" 1)[0m
[1m(insertion-code-from-serial-number 0 "A" 1)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 2)[0m
[1m(seqnum-from-serial-number 0 "A" 2)[0m
[1m(insertion-code-from-serial-number 0 "A" 2)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 3)[0m
[1m(seqnum-from-serial-number 0 "A" 3)[0m
[1m(insertion-code-from-serial-number 0 "A" 3)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 4)[0m
[1m(seqnum-from-serial-number 0 "A" 4)[0m
[1m(insertion-code-from-serial-number 0 "A" 4)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 5)[0m
[1m(seqnum-from-serial-number 0 "A" 5)[0m
[1m(insertion-code-from-serial-number 0 "A" 5)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 6)[0m
[1m(seqnum-from-serial-number 0 "A" 6)[0m
[1m(insertion-code-from-serial-number 0 "A" 6)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 7)[0m
[1m(seqnum-from-serial-number 0 "A" 7)[0m
[1m(insertion-code-from-serial-number 0 "A" 7)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 8)[0m
[1m(seqnum-from-serial-number 0 "A" 8)[0m
[1m(insertion-code-from-serial-number 0 "A" 8)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 9)[0m
[1m(seqnum-from-serial-number 0 "A" 9)[0m
[1m(insertion-code-from-serial-number 0 "A" 9)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 10)[0m
[1m(seqnum-from-serial-number 0 "A" 10)[0m
[1m(insertion-code-from-serial-number 0 "A" 10)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 11)[0m
[1m(seqnum-from-serial-number 0 "A" 11)[0m
[1m(insertion-code-from-serial-number 0 "A" 11)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 12)[0m
[1m(seqnum-from-serial-number 0 "A" 12)[0m
[1m(insertion-code-from-serial-number 0 "A" 12)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 13)[0m
[1m(seqnum-from-serial-number 0 "A" 13)[0m
[1m(insertion-code-from-serial-number 0 "A" 13)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 14)[0m
[1m(seqnum-from-serial-number 0 "A" 14)[0m
[1m(insertion-code-from-serial-number 0 "A" 14)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 15)[0m
[1m(seqnum-from-serial-number 0 "A" 15)[0m
[1m(insertion-code-from-serial-number 0 "A" 15)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 16)[0m
[1m(seqnum-from-serial-number 0 "A" 16)[0m
[1m(insertion-code-from-serial-number 0 "A" 16)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 17)[0m
[1m(seqnum-from-serial-number 0 "A" 17)[0m
[1m(insertion-code-from-serial-number 0 "A" 17)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 18)[0m
[1m(seqnum-from-serial-number 0 "A" 18)[0m
[1m(insertion-code-from-serial-number 0 "A" 18)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 19)[0m
[1m(seqnum-from-serial-number 0 "A" 19)[0m
[1m(insertion-code-from-serial-number 0 "A" 19)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 20)[0m
[1m(seqnum-from-serial-number 0 "A" 20)[0m
[1m(insertion-code-from-serial-number 0 "A" 20)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 21)[0m
[1m(seqnum-from-serial-number 0 "A" 21)[0m
[1m(insertion-code-from-serial-number 0 "A" 21)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 22)[0m
[1m(seqnum-from-serial-number 0 "A" 22)[0m
[1m(insertion-code-from-serial-number 0 "A" 22)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 23)[0m
[1m(seqnum-from-serial-number 0 "A" 23)[0m
[1m(insertion-code-from-serial-number 0 "A" 23)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 24)[0m
[1m(seqnum-from-serial-number 0 "A" 24)[0m
[1m(insertion-code-from-serial-number 0 "A" 24)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 25)[0m
[1m(seqnum-from-serial-number 0 "A" 25)[0m
[1m(insertion-code-from-serial-number 0 "A" 25)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 26)[0m
[1m(seqnum-from-serial-number 0 "A" 26)[0m
[1m(insertion-code-from-serial-number 0 "A" 26)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 27)[0m
[1m(seqnum-from-serial-number 0 "A" 27)[0m
[1m(insertion-code-from-serial-number 0 "A" 27)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 28)[0m
[1m(seqnum-from-serial-number 0 "A" 28)[0m
[1m(insertion-code-from-serial-number 0 "A" 28)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 29)[0m
[1m(seqnum-from-serial-number 0 "A" 29)[0m
[1m(insertion-code-from-serial-number 0 "A" 29)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 30)[0m
[1m(seqnum-from-serial-number 0 "A" 30)[0m
[1m(insertion-code-from-serial-number 0 "A" 30)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 31)[0m
[1m(seqnum-from-serial-number 0 "A" 31)[0m
[1m(insertion-code-from-serial-number 0 "A" 31)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 32)[0m
[1m(seqnum-from-serial-number 0 "A" 32)[0m
[1m(insertion-code-from-serial-number 0 "A" 32)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 33)[0m
[1m(seqnum-from-serial-number 0 "A" 33)[0m
[1m(insertion-code-from-serial-number 0 "A" 33)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 34)[0m
[1m(seqnum-from-serial-number 0 "A" 34)[0m
[1m(insertion-code-from-serial-number 0 "A" 34)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 35)[0m
[1m(seqnum-from-serial-number 0 "A" 35)[0m
[1m(insertion-code-from-serial-number 0 "A" 35)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 36)[0m
[1m(seqnum-from-serial-number 0 "A" 36)[0m
[1m(insertion-code-from-serial-number 0 "A" 36)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 37)[0m
[1m(seqnum-from-serial-number 0 "A" 37)[0m
[1m(insertion-code-from-serial-number 0 "A" 37)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 38)[0m
[1m(seqnum-from-serial-number 0 "A" 38)[0m
[1m(insertion-code-from-serial-number 0 "A" 38)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 39)[0m
[1m(seqnum-from-serial-number 0 "A" 39)[0m
[1m(insertion-code-from-serial-number 0 "A" 39)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 40)[0m
[1m(seqnum-from-serial-number 0 "A" 40)[0m
[1m(insertion-code-from-serial-number 0 "A" 40)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 41)[0m
[1m(seqnum-from-serial-number 0 "A" 41)[0m
[1m(insertion-code-from-serial-number 0 "A" 41)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 42)[0m
[1m(seqnum-from-serial-number 0 "A" 42)[0m
[1m(insertion-code-from-serial-number 0 "A" 42)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 43)[0m
[1m(seqnum-from-serial-number 0 "A" 43)[0m
[1m(insertion-code-from-serial-number 0 "A" 43)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 44)[0m
[1m(seqnum-from-serial-number 0 "A" 44)[0m
[1m(insertion-code-from-serial-number 0 "A" 44)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 45)[0m
[1m(seqnum-from-serial-number 0 "A" 45)[0m
[1m(insertion-code-from-serial-number 0 "A" 45)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 46)[0m
[1m(seqnum-from-serial-number 0 "A" 46)[0m
[1m(insertion-code-from-serial-number 0 "A" 46)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 47)[0m
[1m(seqnum-from-serial-number 0 "A" 47)[0m
[1m(insertion-code-from-serial-number 0 "A" 47)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 48)[0m
[1m(seqnum-from-serial-number 0 "A" 48)[0m
[1m(insertion-code-from-serial-number 0 "A" 48)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 49)[0m
[1m(seqnum-from-serial-number 0 "A" 49)[0m
[1m(insertion-code-from-serial-number 0 "A" 49)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 50)[0m
[1m(seqnum-from-serial-number 0 "A" 50)[0m
[1m(insertion-code-from-serial-number 0 "A" 50)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 51)[0m
[1m(seqnum-from-serial-number 0 "A" 51)[0m
[1m(insertion-code-from-serial-number 0 "A" 51)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 52)[0m
[1m(seqnum-from-serial-number 0 "A" 52)[0m
[1m(insertion-code-from-serial-number 0 "A" 52)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 53)[0m
[1m(seqnum-from-serial-number 0 "A" 53)[0m
[1m(insertion-code-from-serial-number 0 "A" 53)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 54)[0m
[1m(seqnum-from-serial-number 0 "A" 54)[0m
[1m(insertion-code-from-serial-number 0 "A" 54)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 55)[0m
[1m(seqnum-from-serial-number 0 "A" 55)[0m
[1m(insertion-code-from-serial-number 0 "A" 55)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 56)[0m
[1m(seqnum-from-serial-number 0 "A" 56)[0m
[1m(insertion-code-from-serial-number 0 "A" 56)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 57)[0m
[1m(seqnum-from-serial-number 0 "A" 57)[0m
[1m(insertion-code-from-serial-number 0 "A" 57)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 58)[0m
[1m(seqnum-from-serial-number 0 "A" 58)[0m
[1m(insertion-code-from-serial-number 0 "A" 58)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 59)[0m
[1m(seqnum-from-serial-number 0 "A" 59)[0m
[1m(insertion-code-from-serial-number 0 "A" 59)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 60)[0m
[1m(seqnum-from-serial-number 0 "A" 60)[0m
[1m(insertion-code-from-serial-number 0 "A" 60)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 61)[0m
[1m(seqnum-from-serial-number 0 "A" 61)[0m
[1m(insertion-code-from-serial-number 0 "A" 61)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 62)[0m
[1m(seqnum-from-serial-number 0 "A" 62)[0m
[1m(insertion-code-from-serial-number 0 "A" 62)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 63)[0m
[1m(seqnum-from-serial-number 0 "A" 63)[0m
[1m(insertion-code-from-serial-number 0 "A" 63)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 64)[0m
[1m(seqnum-from-serial-number 0 "A" 64)[0m
[1m(insertion-code-from-serial-number 0 "A" 64)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 65)[0m
[1m(seqnum-from-serial-number 0 "A" 65)[0m
[1m(insertion-code-from-serial-number 0 "A" 65)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 66)[0m
[1m(seqnum-from-serial-number 0 "A" 66)[0m
[1m(insertion-code-from-serial-number 0 "A" 66)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 67)[0m
[1m(seqnum-from-serial-number 0 "A" 67)[0m
[1m(insertion-code-from-serial-number 0 "A" 67)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 68)[0m
[1m(seqnum-from-serial-number 0 "A" 68)[0m
[1m(insertion-code-from-serial-number 0 "A" 68)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 69)[0m
[1m(seqnum-from-serial-number 0 "A" 69)[0m
[1m(insertion-code-from-serial-number 0 "A" 69)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 70)[0m
[1m(seqnum-from-serial-number 0 "A" 70)[0m
[1m(insertion-code-from-serial-number 0 "A" 70)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 71)[0m
[1m(seqnum-from-serial-number 0 "A" 71)[0m
[1m(insertion-code-from-serial-number 0 "A" 71)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 72)[0m
[1m(seqnum-from-serial-number 0 "A" 72)[0m
[1m(insertion-code-from-serial-number 0 "A" 72)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 73)[0m
[1m(seqnum-from-serial-number 0 "A" 73)[0m
[1m(insertion-code-from-serial-number 0 "A" 73)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 74)[0m
[1m(seqnum-from-serial-number 0 "A" 74)[0m
[1m(insertion-code-from-serial-number 0 "A" 74)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 75)[0m
[1m(seqnum-from-serial-number 0 "A" 75)[0m
[1m(insertion-code-from-serial-number 0 "A" 75)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 76)[0m
[1m(seqnum-from-serial-number 0 "A" 76)[0m
[1m(insertion-code-from-serial-number 0 "A" 76)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 77)[0m
[1m(seqnum-from-serial-number 0 "A" 77)[0m
[1m(insertion-code-from-serial-number 0 "A" 77)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 78)[0m
[1m(seqnum-from-serial-number 0 "A" 78)[0m
[1m(insertion-code-from-serial-number 0 "A" 78)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 79)[0m
[1m(seqnum-from-serial-number 0 "A" 79)[0m
[1m(insertion-code-from-serial-number 0 "A" 79)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 80)[0m
[1m(seqnum-from-serial-number 0 "A" 80)[0m
[1m(insertion-code-from-serial-number 0 "A" 80)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 81)[0m
[1m(seqnum-from-serial-number 0 "A" 81)[0m
[1m(insertion-code-from-serial-number 0 "A" 81)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 82)[0m
[1m(seqnum-from-serial-number 0 "A" 82)[0m
[1m(insertion-code-from-serial-number 0 "A" 82)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 83)[0m
[1m(seqnum-from-serial-number 0 "A" 83)[0m
[1m(insertion-code-from-serial-number 0 "A" 83)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 84)[0m
[1m(seqnum-from-serial-number 0 "A" 84)[0m
[1m(insertion-code-from-serial-number 0 "A" 84)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 85)[0m
[1m(seqnum-from-serial-number 0 "A" 85)[0m
[1m(insertion-code-from-serial-number 0 "A" 85)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 86)[0m
[1m(seqnum-from-serial-number 0 "A" 86)[0m
[1m(insertion-code-from-serial-number 0 "A" 86)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 87)[0m
[1m(seqnum-from-serial-number 0 "A" 87)[0m
[1m(insertion-code-from-serial-number 0 "A" 87)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 88)[0m
[1m(seqnum-from-serial-number 0 "A" 88)[0m
[1m(insertion-code-from-serial-number 0 "A" 88)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 89)[0m
[1m(seqnum-from-serial-number 0 "A" 89)[0m
[1m(insertion-code-from-serial-number 0 "A" 89)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 90)[0m
[1m(seqnum-from-serial-number 0 "A" 90)[0m
[1m(insertion-code-from-serial-number 0 "A" 90)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 91)[0m
[1m(seqnum-from-serial-number 0 "A" 91)[0m
[1m(insertion-code-from-serial-number 0 "A" 91)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 92)[0m
[1m(seqnum-from-serial-number 0 "A" 92)[0m
[1m(insertion-code-from-serial-number 0 "A" 92)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 93)[0m
[1m(seqnum-from-serial-number 0 "A" 93)[0m
[1m(insertion-code-from-serial-number 0 "A" 93)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 94)[0m
[1m(seqnum-from-serial-number 0 "A" 94)[0m
[1m(insertion-code-from-serial-number 0 "A" 94)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 95)[0m
[1m(seqnum-from-serial-number 0 "A" 95)[0m
[1m(insertion-code-from-serial-number 0 "A" 95)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(resname-from-serial-number 0 "A" 96)[0m
[1m(seqnum-from-serial-number 0 "A" 96)[0m
[1m(insertion-code-from-serial-number 0 "A" 96)[0m
----------------- in create_mmdbmanager_from_res_vector() alt_conf is ""
----------------- in create_mmdbmanager_from_res_vector() use_alt_conf is 0""
------------ ERROR! -------------------
moving_atoms_asc_type not known: 0
------------ ERROR! -------------------
debug:: in clear_all_atom_pull_restraints() 0
debug:: g.safe_scheme_command() with command post-manipulation-hook
[1m(write-pdb-file 0 "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb")[0m
[1m(close-molecule 0)[0m
[1m(close-molecule 1)[0m
[1m(stereo-mode-state)[0m
State file 0-coot.state.scm written.
[1m(stereo-mode-state)[0m
State file 0-coot.state.py written.
[1m(save-state)[0m
State file 0-coot-history.py written.
State file 0-coot-history.scm written.
Starting phenix.real_space_refine (version: 1.20)
on Fri Jun 9 14:26:00 2023 by webdklab
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb
Found real_map, /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
resolution=3.7000
output.suffix=_phenix_refine
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
default_real_map = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/mask_map.mrc"
model {
file = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb"
}
default_model = "/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle2.pdb"
}
resolution = 3.7000
output {
suffix = _phenix_refine
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.038
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.00s
Monomer Library directory:
"/apps/phenix/phenix-1.20-4459/modules/chem_data/mon_lib"
Total number of atoms: 2035
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2035
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 97, 2035
Classifications: {'RNA': 97}
Modifications used: {'rna3p_pyr': 1, 'rna2p_pur': 35, 'rna3p_pur': 1, 'rna2p_pyr': 60}
Link IDs: {'rna3p': 2, 'rna2p': 94}
Chain breaks: 20
Time building chain proxies: 0.42, per 1000 atoms: 0.21
Number of scatterers: 2035
At special positions: 0
Unit cell: (50, 58, 137, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
P 97 15.00
O 697 8.00
N 332 7.00
C 909 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.31
Conformation dependent library (CDL) restraints added in 4.5 milliseconds
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 0
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 0 sheets defined
0.0% alpha, 0.0% beta
15 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.17
Creating SS restraints...
No hydrogen bonds defined for protein.
Restraints generated for nucleic acids:
32 hydrogen bonds
38 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 0.13
Time building geometry restraints manager: 0.33 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.37: 624
1.37 - 1.55: 1428
1.55 - 1.72: 180
1.72 - 1.89: 10
1.89 - 2.07: 2
Bond restraints: 2244
Sorted by residual:
bond pdb="C1' U A 4 "
pdb="N1 U A 4 "
ideal model delta sigma weight residual
1.480 2.068 -0.588 1.50e-02 4.44e+03 1.54e+03
bond pdb="P C A 54 "
pdb="O5' C A 54 "
ideal model delta sigma weight residual
1.593 2.000 -0.407 1.50e-02 4.44e+03 7.35e+02
bond pdb="N1 G A 3 "
pdb="C2 G A 3 "
ideal model delta sigma weight residual
1.373 1.879 -0.506 2.00e-02 2.50e+03 6.40e+02
bond pdb="C2 C A 53 "
pdb="N3 C A 53 "
ideal model delta sigma weight residual
1.353 1.831 -0.478 2.00e-02 2.50e+03 5.72e+02
bond pdb="C6 G A 3 "
pdb="N1 G A 3 "
ideal model delta sigma weight residual
1.391 1.861 -0.470 2.00e-02 2.50e+03 5.52e+02
... (remaining 2239 not shown)
Histogram of bond angle deviations from ideal:
69.81 - 87.35: 52
87.35 - 104.90: 384
104.90 - 122.44: 2520
122.44 - 139.99: 479
139.99 - 157.54: 5
Bond angle restraints: 3440
Sorted by residual:
angle pdb="P C A 54 "
pdb="O5' C A 54 "
pdb="C5' C A 54 "
ideal model delta sigma weight residual
120.90 150.09 -29.19 1.50e+00 4.44e-01 3.79e+02
angle pdb="C2 U A 4 "
pdb="N1 U A 4 "
pdb="C6 U A 4 "
ideal model delta sigma weight residual
121.00 70.79 50.21 3.00e+00 1.11e-01 2.80e+02
angle pdb="OP1 C A 20 "
pdb="P C A 20 "
pdb="OP2 C A 20 "
ideal model delta sigma weight residual
119.60 77.12 42.48 3.00e+00 1.11e-01 2.01e+02
angle pdb="OP1 G A 52 "
pdb="P G A 52 "
pdb="OP2 G A 52 "
ideal model delta sigma weight residual
119.60 78.40 41.20 3.00e+00 1.11e-01 1.89e+02
angle pdb="C2' G A 3 "
pdb="C1' G A 3 "
pdb="N9 G A 3 "
ideal model delta sigma weight residual
112.00 131.74 -19.74 1.50e+00 4.44e-01 1.73e+02
... (remaining 3435 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.97: 846
35.97 - 71.95: 190
71.95 - 107.92: 48
107.92 - 143.89: 11
143.89 - 179.87: 6
Dihedral angle restraints: 1101
sinusoidal: 1101
harmonic: 0
Sorted by residual:
dihedral pdb="C4' G A 3 "
pdb="C3' G A 3 "
pdb="C2' G A 3 "
pdb="C1' G A 3 "
ideal model delta sinusoidal sigma weight residual
36.00 -30.56 66.56 1 8.00e+00 1.56e-02 9.03e+01
dihedral pdb="C4' U A 4 "
pdb="C3' U A 4 "
pdb="C2' U A 4 "
pdb="C1' U A 4 "
ideal model delta sinusoidal sigma weight residual
36.00 -24.80 60.80 1 8.00e+00 1.56e-02 7.68e+01
dihedral pdb="O4' G A 3 "
pdb="C2' G A 3 "
pdb="C1' G A 3 "
pdb="C3' G A 3 "
ideal model delta sinusoidal sigma weight residual
25.00 -35.29 60.29 1 8.00e+00 1.56e-02 7.57e+01
... (remaining 1098 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.741: 458
0.741 - 1.481: 25
1.481 - 2.221: 1
2.221 - 2.961: 0
2.961 - 3.702: 1
Chirality restraints: 485
Sorted by residual:
chirality pdb="C1' G A 3 "
pdb="O4' G A 3 "
pdb="C2' G A 3 "
pdb="N9 G A 3 "
both_signs ideal model delta sigma weight residual
False 2.46 -1.24 3.70 2.00e-01 2.50e+01 3.43e+02
chirality pdb="P A A 81 "
pdb="OP1 A A 81 "
pdb="OP2 A A 81 "
pdb="O5' A A 81 "
both_signs ideal model delta sigma weight residual
True 2.41 -0.83 1.58 2.00e-01 2.50e+01 6.26e+01
chirality pdb="P G A 37 "
pdb="OP1 G A 37 "
pdb="OP2 G A 37 "
pdb="O5' G A 37 "
both_signs ideal model delta sigma weight residual
True 2.41 -0.96 1.45 2.00e-01 2.50e+01 5.23e+01
... (remaining 482 not shown)
Planarity restraints: 97
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb="C1' G A 3 " -0.084 2.00e-02 2.50e+03 4.21e-02 5.31e+01
pdb="N9 G A 3 " 0.078 2.00e-02 2.50e+03
pdb="C8 G A 3 " 0.054 2.00e-02 2.50e+03
pdb="N7 G A 3 " 0.007 2.00e-02 2.50e+03
pdb="C5 G A 3 " -0.019 2.00e-02 2.50e+03
pdb="C6 G A 3 " -0.029 2.00e-02 2.50e+03
pdb="O6 G A 3 " 0.004 2.00e-02 2.50e+03
pdb="N1 G A 3 " -0.030 2.00e-02 2.50e+03
pdb="C2 G A 3 " 0.046 2.00e-02 2.50e+03
pdb="N2 G A 3 " 0.001 2.00e-02 2.50e+03
pdb="N3 G A 3 " 0.003 2.00e-02 2.50e+03
pdb="C4 G A 3 " -0.031 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' U A 24 " 0.030 2.00e-02 2.50e+03 2.06e-02 9.54e+00
pdb="N1 U A 24 " -0.035 2.00e-02 2.50e+03
pdb="C2 U A 24 " 0.007 2.00e-02 2.50e+03
pdb="O2 U A 24 " -0.000 2.00e-02 2.50e+03
pdb="N3 U A 24 " -0.008 2.00e-02 2.50e+03
pdb="C4 U A 24 " -0.024 2.00e-02 2.50e+03
pdb="O4 U A 24 " 0.031 2.00e-02 2.50e+03
pdb="C5 U A 24 " 0.000 2.00e-02 2.50e+03
pdb="C6 U A 24 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb="C1' C A 13 " 0.024 2.00e-02 2.50e+03 1.58e-02 5.60e+00
pdb="N1 C A 13 " -0.029 2.00e-02 2.50e+03
pdb="C2 C A 13 " 0.003 2.00e-02 2.50e+03
pdb="O2 C A 13 " -0.003 2.00e-02 2.50e+03
pdb="N3 C A 13 " 0.006 2.00e-02 2.50e+03
pdb="C4 C A 13 " -0.021 2.00e-02 2.50e+03
pdb="N4 C A 13 " 0.018 2.00e-02 2.50e+03
pdb="C5 C A 13 " 0.002 2.00e-02 2.50e+03
pdb="C6 C A 13 " 0.000 2.00e-02 2.50e+03
... (remaining 94 not shown)
Histogram of nonbonded interaction distances:
1.68 - 2.32: 94
2.32 - 2.97: 1257
2.97 - 3.61: 3978
3.61 - 4.26: 5315
4.26 - 4.90: 7020
Nonbonded interactions: 17664
Sorted by model distance:
nonbonded pdb="N1 C A 53 "
pdb="O5' C A 54 "
model vdw
1.677 3.120
nonbonded pdb="N1 G A 3 "
pdb="N1 U A 4 "
model vdw
1.685 3.200
nonbonded pdb="N3 C A 53 "
pdb="O5' C A 54 "
model vdw
1.739 3.120
nonbonded pdb="C2 C A 53 "
pdb="O5' C A 54 "
model vdw
1.746 3.260
nonbonded pdb="C2 G A 3 "
pdb="N1 U A 4 "
model vdw
1.761 3.340
... (remaining 17659 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
P 97 5.49 5
C 909 2.51 5
N 332 2.21 5
O 697 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 5
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Write .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.540
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 1.000
Check model and map are aligned: 0.010
Convert atoms to be neutral: 0.010
Process input model: 2.860
Find NCS groups from input model: 0.010
Set up NCS constraints: 0.000
Set refine NCS operators: 0.000
Set scattering table: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:0.720
Set ADP refinement strategy: 0.000
Write .geo file: 1.170
Internal consistency checks: 0.000
Total: 6.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.588 2244 Z= 2.080
Angle : 5.098 50.215 3440 Z= 1.895
Chirality : 0.348 3.702 485
Planarity : 0.008 0.042 97
Dihedral : 34.403 179.867 1101
Min Nonbonded Distance : 1.677
Molprobity Statistics.
All-atom Clashscore : 89.43
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0176
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.6980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 6.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.6738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start: 0.2071
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.599 2244 Z= 2.064
Angle : 4.137 49.444 3440 Z= 1.568
Chirality : 0.451 3.878 485
Planarity : 0.007 0.032 97
Dihedral : 33.670 177.120 1101
Min Nonbonded Distance : 1.663
Molprobity Statistics.
All-atom Clashscore : 86.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.034
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0271
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.016
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0069
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 50.0000
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 2.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 3.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start: 0.5577
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.598 2244 Z= 2.069
Angle : 4.156 49.090 3440 Z= 1.568
Chirality : 0.444 3.887 485
Planarity : 0.007 0.032 97
Dihedral : 33.481 173.787 1101
Min Nonbonded Distance : 1.670
Molprobity Statistics.
All-atom Clashscore : 92.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0175
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0064
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 40.0000
chunk 1 optimal weight: 0.6980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 3.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 8.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.9238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start: 0.6666
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.591 2244 Z= 2.065
Angle : 4.133 49.205 3440 Z= 1.564
Chirality : 0.446 3.905 485
Planarity : 0.007 0.033 97
Dihedral : 33.179 178.666 1101
Min Nonbonded Distance : 1.665
Molprobity Statistics.
All-atom Clashscore : 94.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.014
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0176
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 1.9990
chunk 1 optimal weight: 1.9990
chunk 2 optimal weight: 0.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 4.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.7490
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start: 0.8383
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.585 2244 Z= 2.062
Angle : 3.950 49.218 3440 Z= 1.504
Chirality : 0.446 3.954 485
Planarity : 0.007 0.028 97
Dihedral : 32.960 177.589 1101
Min Nonbonded Distance : 1.666
Molprobity Statistics.
All-atom Clashscore : 88.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
0 Ramachandran restraints generated.
0 Oldfield, 0 Emsley, 0 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Fit side-chains
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0170
Evaluate side-chains
0 residues out of total 0 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 0
time to evaluate : 0.013
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 0.0061
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 9
random chunks:
chunk 0 optimal weight: 40.0000
chunk 1 optimal weight: 0.5980
chunk 2 optimal weight: 1.9990
chunk 3 optimal weight: 2.9990
chunk 4 optimal weight: 3.9990
chunk 5 optimal weight: 5.9990
chunk 6 optimal weight: 2.9990
chunk 7 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
overall best weight: 1.8988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.107818 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.095179 restraints weight = 11644.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.096973 restraints weight = 4989.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.098160 restraints weight = 2997.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start: 0.8868
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.036 0.597 2244 Z= 2.070
Angle : 3.939 49.217 3440 Z= 1.500
Chirality : 0.447 3.891 485
Planarity : 0.007 0.031 97
Dihedral : 32.981 178.740 1101
Min Nonbonded Distance : 1.666
Molprobity Statistics.
All-atom Clashscore : 94.35
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: None (None), residues: 0
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : None (None), residues: 0
===============================================================================
Job complete
usr+sys time: 145.60 seconds
wall clock time: 4 minutes 32.11 seconds (272.11 seconds total)
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 10.167250633239746
dmean : 5.7266399380750954e-05
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.023769386112689972
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:18:59 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
in total 86 isolated grid points
we have 0/174 base assignment outside safe range: 0.000
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/base_assignsugar_combine created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq created
we have 1/122 base assignment outside safe range: 0.008
we have 1/122 base assignment outside safe range: 0.008
only apply geometry constraints for dynamic programming
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0 created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0/path_order created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/DP_geo_match/path_0/path_reverse_order created
geometrical based dp finished selecting ldp for atomic modeling
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo created
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/graph_atomic_modeling/Output_Structure_noseq/AssembleFactory_geo/atomic_geo/Path_Atomic_Frags created
duplicate use of 13/98 pho positions in atomic
revise 25/98 pho positions in atomic
{3, 4, 6, 7, 8, 10, 12, 13, 21, 33, 34, 37, 38, 39, 41, 42, 45, 46, 54, 55, 56, 59, 60, 61, 99}
previous loc [141.22828214631141, 114.06837996436745, 101.35129613280449] updated loc: [141.22828214631141, 114.06837996436745, 101.35129613280449]
previous loc [117.78454159852292, 129.18897958649018, 156.73330225140765] updated loc: [117.90138026042874, 131.23901906657989, 155.40754600245518]
previous loc [117.78454159852292, 129.18897958649018, 156.73330225140765] updated loc: [117.78454159852292, 129.18897958649018, 156.73330225140765]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [130.26950048795507, 123.99012598291503, 164.17721879440776] updated loc: [130.26950048795507, 123.99012598291503, 164.17721879440776]
previous loc [136.87420336217642, 133.7489795495849, 170.55259591110692] updated loc: [136.87420336217642, 133.7489795495849, 170.55259591110692]
previous loc [136.87420336217642, 133.7489795495849, 170.55259591110692] updated loc: [136.87420336217642, 133.7489795495849, 170.55259591110692]
previous loc [126.66219761035069, 138.1737504527791, 181.89940763032868] updated loc: [128.4402524368203, 140.18530774000502, 179.2941443882781]
previous loc [126.66219761035069, 138.1737504527791, 181.89940763032868] updated loc: [126.27207221165374, 135.6400451342626, 183.4575478552197]
previous loc [141.8872530017751, 131.2376876647608, 177.46735245256994] updated loc: [141.38606830362136, 134.0230962905337, 180.1413201291402]
duplicate use of 5/98 pho positions in atomic
round 2 we still put 3 points into clear set
clearning changed 181 to 178 frag info
Reflection detected
Reflection detected
use pho situation 6
Reflection detected
use pho situation 2
use pho situation 7
Reflection detected
use pho situation 6
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
Reflection detected
use pho situation 7
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
use pho situation 5
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 2
use pho situation 7
use pho situation 6
Reflection detected
use pho situation 1
use pho situation 2
Reflection detected
use pho situation 5
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 2
Reflection detected
use pho situation 7
Reflection detected
Reflection detected
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 2
use pho situation 7
Reflection detected
use pho situation 6
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
Reflection detected
use pho situation 1
use pho situation 2
use pho situation 9
Reflection detected
we have 94/98 atomic build upon pho atoms
!!!parsing fasta input failed, we can not output structures considering sequence assignment!!!
Origin: (0., 0., 0.)
Previous voxel size: (1., 1., 1.)
nx, ny, nz 271 271 271
nxs,nys,nzs 0 0 0
mx,my,mz 271 271 271
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : -2.0060575008392334
dmax : 3.1596052646636963
dmean : 0.012243181467056274
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.09513364732265472
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 13:50:13 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
nx : 271
ny : 271
nz : 271
mode : 2
nxstart : 0
nystart : 0
nzstart : 0
mx : 271
my : 271
mz : 271
cella : (271., 271., 271.)
cellb : (90., 90., 90.)
mapc : 1
mapr : 2
maps : 3
dmin : 0.0
dmax : 3.1596052646636963
dmean : 0.001319283852353692
ispg : 1
nsymbt : 0
extra1 : b'\x00\x00\x00\x00\x00\x00\x00\x00'
exttyp : b''
nversion : 20141
extra2 : b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'
origin : (0., 0., 0.)
map : b'MAP '
machst : [68 68 0 0]
rms : 0.037648122757673264
nlabl : 1
label : [b'Created by mrcfile.py 2023-06-09 14:19:06 '
b'' b'' b'' b'' b'' b'' b'' b'' b'']
/bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output created
please check final refined atomic structure in /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output/Refine_cycle3.pdb
You can also check other refined output here /bio/kihara-web/www/em/em-web-server/media/jobs/output/10043363bd0b413a007d1f8f2150caf7/Output
INFO : CryoREAD Done
If the output looks wrong or the job has failed. You can submit it for review here.