daq-refine

Job ID : 9d089ca034a9340fc99ca25a77b27bc2

DAQ-refine is a tool that assesses protein models derived from cryo-EM maps (target resolution: 0-5 A) using the DAQ score and refine the identified regions with errors with modified AlphaFold2.
The output includes a .pdb file documenting the initially scored structure (by DAQ-Score) alongside the refined structure generated by DAQ-Refine.

Our result webpage comprises three tabs: Results Visualization, Output Logs, and Job Configuration.

Results Visualization:
The 'Result Visualization' panel displays both the protein structure before and after refinement by DAQ-Refine.
The B-factor column stores the DAQ(AA) score for each structure.
On the right-hand side, you can click the 'Download Outputs' button to acquire the modeled structure in .pdb format.
The downloaded file includes the original input structure as the 1st model and the refined structure by DAQ-Refine as the 2nd model.
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.

The 3D models displayed in the panel are color-coded based on the DAQ(AA) score, ranging from red (-1.0) to blue (1.0), employing a 19-residue sliding window. Blue represents a good score, while red signifies a lower score from DAQ.
In MODEL1, the original model depicts all modeled positions colored according to the DAQ(AA) score.
In MODEL2, the DAQ-Refine refined model portrays all modeled positions color-coded based on the DAQ(AA) score.

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.

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 'DAQ-Refine 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, gterashi@purdue.edu, xiaowang20140001@gmail.com.

DAQ-refine is a protocol using DAQ score to evaluate protein models from cryo-EM maps and employs a modified AlphaFold 2 for refining regions with potential errors.
The 3D model is colored by DAQ(AA) score scaled from red (-1.0) to blue (1.0) with a 19 residues sliding window. Here blue indicates good score, while red indicates bad score from DAQ.
In MODEL1, it shows the original model, all modeled positions are colored by DAQ(AA) score.
In MODEL2, it shows the DAQ refined model, all modeled positions are colored by DAQ(AA) score.
If you encounter any questions for the scored structure, feel free to email dkihara@purdue.edu, gterashi@purdue.edu and wang3702@purdue.edu.

INFO : DAQ-refine started
INFO : STEP-0 DAQ started
INFO: start DAQ-refine for chain 9
gcc -O3 -c chkcmdline.c
gcc -O3 -c mrc.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -O3 -c readpdb.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -o TrimMapAtom main.c chkcmdline.o mrc.o readpdb.o -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
/net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9 existed
----------------------------------------------------------------------------------------------------
resizing finished!
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Finished processing model input!
0 batch processing time 0.095970
1 batch processing time 0.089430
2 batch processing time 0.089174
3 batch processing time 0.091266
4 batch processing time 0.090428
5 batch processing time 0.089364
6 batch processing time 0.088835
7 batch processing time 0.089340
8 batch processing time 0.090916
9 batch processing time 0.088651
10 batch processing time 0.089578
11 batch processing time 0.089557
12 batch processing time 0.089761
13 batch processing time 0.089898
14 batch processing time 0.089353
15 batch processing time 0.089113
16 batch processing time 0.089424
17 batch processing time 0.089744
18 batch processing time 0.089956
19 batch processing time 0.090555
20 batch processing time 0.089671
21 batch processing time 0.088907
22 batch processing time 0.090047
23 batch processing time 0.089864
24 batch processing time 0.090129
25 batch processing time 0.090763
26 batch processing time 0.089237
27 batch processing time 0.092796
28 batch processing time 0.090969
29 batch processing time 0.089121
30 batch processing time 0.090451
31 batch processing time 0.090422
32 batch processing time 0.090296
33 batch processing time 0.090188
34 batch processing time 0.090152
35 batch processing time 0.089834
36 batch processing time 0.089702
37 batch processing time 0.089639
38 batch processing time 0.089392
39 batch processing time 0.089892
40 batch processing time 0.089940
41 batch processing time 0.089653
42 batch processing time 0.091637
43 batch processing time 0.089039
44 batch processing time 0.089026
45 batch processing time 0.089657
46 batch processing time 0.089252
47 batch processing time 0.089935
48 batch processing time 0.089663
49 batch processing time 0.089823
50 batch processing time 0.090587
51 batch processing time 0.091804
52 batch processing time 0.089776
53 batch processing time 0.090572
54 batch processing time 0.090062
55 batch processing time 0.090609
56 batch processing time 0.090005
57 batch processing time 0.089090
58 batch processing time 0.090024
59 batch processing time 0.089700
60 batch processing time 0.089526
61 batch processing time 0.089203
62 batch processing time 0.090047
63 batch processing time 0.089225
64 batch processing time 0.089511
65 batch processing time 0.089699
66 batch processing time 0.089272
67 batch processing time 0.089239
68 batch processing time 0.089219
69 batch processing time 0.090436
70 batch processing time 0.090308
71 batch processing time 0.089883
72 batch processing time 0.088973
73 batch processing time 0.089257
74 batch processing time 0.090553
75 batch processing time 0.092682
76 batch processing time 0.090390
77 batch processing time 0.090000
78 batch processing time 0.089700
79 batch processing time 0.090446
80 batch processing time 0.089489
81 batch processing time 0.089383
82 batch processing time 0.090330
83 batch processing time 0.089751
84 batch processing time 0.089252
85 batch processing time 0.089679
86 batch processing time 0.089230
87 batch processing time 0.090802
88 batch processing time 0.090221
89 batch processing time 0.089739
90 batch processing time 0.090125
91 batch processing time 0.089924
92 batch processing time 0.089616
93 batch processing time 0.090271
94 batch processing time 0.090100
95 batch processing time 0.090194
96 batch processing time 0.089455
97 batch processing time 0.089612
98 batch processing time 0.092499
99 batch processing time 0.091762
100 batch processing time 0.089199
101 batch processing time 0.089732
102 batch processing time 0.089648
103 batch processing time 0.090079
104 batch processing time 0.090486
105 batch processing time 0.090511
106 batch processing time 0.089198
107 batch processing time 0.089466
108 batch processing time 0.090092
109 batch processing time 0.089109
110 batch processing time 0.089768
111 batch processing time 0.089628
112 batch processing time 0.089213
113 batch processing time 0.089566
Our predictions are saved in /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/prediction.txt, please have a check!
total different chains: {'9'}
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[['9', ' N ', 382.096, 210.325, 173.282], ['9', ' CA ', 382.772, 209.03, 173.465], ['9', ' C ', 383.946, 209.064, 174.454], ['9', ' O ', 384.602, 208.043, 174.668], ['9', ' CB ', 383.286, 208.519, 172.114], ['9', ' CG ', 382.245, 208.515, 171.004], ['9', ' CD ', 382.808, 207.954, 169.708], ['9', ' CE ', 381.775, 207.997, 168.591], ['9', ' NZ ', 382.268, 207.348, 167.346], ['9', ' H ', 382.697, 211.037, 172.891], ['9', ' HA ', 382.131, 208.369, 173.799], ['9', ' HB2', 384.019, 209.086, 171.826], ['9', ' HB3', 383.6, 207.608, 172.224], ['9', ' HG2', 381.493, 207.964, 171.273], ['9', ' HG3', 381.951, 209.423, 170.833], ['9', ' HD2', 383.573, 208.484, 169.435], ['9', ' HD3', 383.07, 207.03, 169.845], ['9', ' HE2', 380.976, 207.529, 168.879], ['9', ' HE3', 381.565, 208.922, 168.387], ['9', ' HZ1', 383.062, 207.791, 167.037], ['9', ' HZ2', 381.597, 207.399, 166.662], ['9', ' HZ3', 382.472, 206.425, 167.515]]
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[['9', ' N ', 381.518, 213.533, 180.893], ['9', ' CA ', 381.096, 214.932, 180.973], ['9', ' C ', 380.014, 215.176, 182.032], ['9', ' O ', 379.875, 216.3, 182.516], ['9', ' CB ', 380.591, 215.445, 179.607], ['9', ' CG1', 381.628, 215.176, 178.508], ['9', ' CG2', 380.268, 216.933, 179.672], ['9', ' CD1', 382.928, 215.946, 178.649], ['9', ' H ', 380.796, 212.904, 180.576], ['9', ' HA ', 381.861, 215.488, 181.227], ['9', ' HB ', 379.778, 214.965, 179.384], ['9', 'HG12', 381.846, 214.233, 178.511], ['9', 'HG13', 381.242, 215.415, 177.652], ['9', 'HG21', 379.361, 217.045, 179.968], ['9', 'HG22', 380.372, 217.316, 178.798], ['9', 'HG23', 380.869, 217.363, 180.285], ['9', 'HD11', 382.75, 216.887, 178.583], ['9', 'HD12', 383.52, 215.679, 177.942], ['9', 'HD13', 383.329, 215.747, 179.497]]
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[['9', ' N ', 375.809, 214.434, 178.936], ['9', ' CA ', 375.545, 213.974, 177.57], ['9', ' C ', 375.331, 212.475, 177.512], ['9', ' O ', 375.888, 211.728, 178.322], ['9', ' CB ', 376.702, 214.314, 176.62], ['9', ' CG ', 377.118, 215.766, 176.357], ['9', ' CD1', 375.954, 216.722, 176.554], ['9', ' CD2', 378.295, 216.168, 177.232], ['9', ' H ', 376.769, 214.687, 179.111], ['9', ' HA ', 374.731, 214.406, 177.237], ['9', ' HB2', 377.487, 213.849, 176.95], ['9', ' HB3', 376.474, 213.946, 175.752], ['9', ' HG ', 377.404, 215.841, 175.433], ['9', 'HD11', 375.179, 216.362, 176.124], ['9', 'HD12', 376.178, 217.574, 176.173], ['9', 'HD13', 375.786, 216.814, 177.494], ['9', 'HD21', 377.997, 216.26, 178.138], ['9', 'HD22', 378.644, 217.004, 176.916], ['9', 'HD23', 378.975, 215.493, 177.176]]
[['9', ' N ', 374.531, 212.041, 176.54], ['9', ' CA ', 374.412, 210.623, 176.244], ['9', ' C ', 375.601, 210.235, 175.384], ['9', ' O ', 376.038, 211.005, 174.526], ['9', ' CB ', 373.076, 210.285, 175.563], ['9', ' CG ', 373.043, 210.303, 174.04], ['9', ' CD ', 371.889, 209.449, 173.538], ['9', ' NE ', 371.779, 209.458, 172.082], ['9', ' CZ ', 371.034, 208.611, 171.374], ['9', ' NH1', 370.314, 207.665, 171.972], ['9', ' NH2', 371.007, 208.709, 170.05], ['9', ' H ', 373.97, 212.639, 175.95], ['9', ' HA ', 374.452, 210.11, 177.079], ['9', ' HB2', 372.815, 209.396, 175.846], ['9', ' HB3', 372.412, 210.923, 175.865], ['9', ' HG2', 372.913, 211.212, 173.728], ['9', ' HG3', 373.857, 209.93, 173.674], ['9', ' HD2', 372.038, 208.535, 173.825], ['9', ' HD3', 371.058, 209.785, 173.908], ['9', ' HE ', 372.089, 210.258, 171.63], ['9', 'HH11', 370.315, 207.584, 172.827], ['9', 'HH12', 369.838, 207.127, 171.5], ['9', 'HH21', 371.468, 209.316, 169.651], ['9', 'HH22', 370.528, 208.166, 169.586]]
[['9', ' N ', 376.133, 209.046, 175.635], ['9', ' CA ', 377.281, 208.555, 174.894], ['9', ' C ', 376.85, 207.916, 173.583], ['9', ' O ', 375.66, 207.704, 173.341], ['9', ' CB ', 378.052, 207.526, 175.724], ['9', ' CG ', 378.859, 208.109, 176.87], ['9', ' CD ', 379.525, 206.999, 177.668], ['9', ' NE ', 380.672, 207.466, 178.444], ['9', ' CZ ', 380.597, 208.185, 179.564], ['9', ' NH1', 379.423, 208.56, 180.067], ['9', ' NH2', 381.713, 208.544, 180.184], ['9', ' H ', 375.786, 208.407, 176.337], ['9', ' HA ', 377.881, 209.3, 174.694], ['9', ' HB2', 377.424, 206.889, 176.1], ['9', ' HB3', 378.675, 207.06, 175.145], ['9', ' HG2', 379.551, 208.689, 176.518], ['9', ' HG3', 378.269, 208.604, 177.458], ['9', ' HD2', 378.879, 206.609, 178.277], ['9', ' HD3', 379.846, 206.32, 177.054], ['9', ' HE ', 381.553, 207.274, 178.088], ['9', 'HH11', 378.687, 208.339, 179.686], ['9', 'HH12', 379.398, 209.026, 180.789], ['9', 'HH21', 382.478, 208.311, 179.868], ['9', 'HH22', 381.675, 209.012, 180.905]]
[['9', ' N ', 377.832, 207.629, 172.732], ['9', ' CA ', 377.634, 206.711, 171.618], ['9', ' C ', 377.302, 205.341, 172.216], ['9', ' O ', 378.03, 204.867, 173.091], ['9', ' CB ', 378.906, 206.619, 170.77], ['9', ' CG ', 378.819, 205.552, 169.691], ['9', ' OD1', 377.976, 205.693, 168.78], ['9', ' OD2', 379.6, 204.578, 169.749], ['9', ' H ', 378.762, 208.018, 172.792], ['9', ' HA ', 376.899, 207.027, 171.057], ['9', ' HB2', 379.058, 207.472, 170.334], ['9', ' HB3', 379.656, 206.402, 171.346]]
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[['9', ' N ', 376.165, 167.384, 190.867], ['9', ' CA ', 377.225, 167.164, 189.881], ['9', ' C ', 378.383, 168.119, 190.127], ['9', ' O ', 379.557, 167.72, 190.136], ['9', ' H ', 375.275, 167.611, 190.447], ['9', ' HA2', 377.548, 166.251, 189.936], ['9', ' HA3', 376.872, 167.323, 188.995]]
[['9', ' N ', 378.019, 169.381, 190.332], ['9', ' CA ', 378.985, 170.453, 190.592], ['9', ' C ', 379.805, 170.132, 191.842], ['9', ' O ', 381.033, 170.254, 191.847], ['9', ' CB ', 378.284, 171.808, 190.749], ['9', ' OG ', 379.203, 172.821, 191.121], ['9', ' H ', 377.061, 169.701, 190.318], ['9', ' HA ', 379.602, 170.518, 189.834], ['9', ' HB2', 377.876, 172.049, 189.902], ['9', ' HB3', 377.603, 171.738, 191.434], ['9', ' HG ', 378.782, 173.554, 191.262]]
[['9', ' N ', 379.095, 169.73, 192.902], ['9', ' CA ', 379.666, 169.508, 194.241], ['9', ' C ', 380.146, 168.064, 194.461], ['9', ' O ', 379.915, 167.481, 195.523], ['9', ' CB ', 378.628, 169.869, 195.319], ['9', ' CG ', 378.404, 171.337, 195.691], ['9', ' CD1', 378.148, 172.239, 194.49], ['9', ' CD2', 377.247, 171.425, 196.678], ['9', ' H ', 378.103, 169.547, 192.862], ['9', ' HA ', 380.437, 170.101, 194.364], ['9', ' HB2', 377.769, 169.516, 195.041], ['9', ' HB3', 378.886, 169.435, 196.147], ['9', ' HG ', 379.198, 171.667, 196.141], ['9', 'HD11', 378.835, 172.108, 193.835], ['9', 'HD12', 378.155, 173.152, 194.785], ['9', 'HD13', 377.291, 172.028, 194.117], ['9', 'HD21', 376.449, 171.104, 196.252], ['9', 'HD22', 377.132, 172.34, 196.943], ['9', 'HD23', 377.45, 170.884, 197.445]]
[['9', ' N ', 380.819, 167.495, 193.464], ['9', ' CA ', 381.36, 166.144, 193.572], ['9', ' C ', 382.683, 166.176, 194.335], ['9', ' O ', 383.57, 166.968, 194.01], ['9', ' CB ', 381.575, 165.544, 192.18], ['9', ' H ', 381.016, 167.935, 192.578], ['9', ' HA ', 380.728, 165.57, 194.053], ['9', ' HB2', 380.726, 165.521, 191.712], ['9', ' HB3', 382.128, 166.13, 191.648]]
[['9', ' N ', 382.81, 165.318, 195.347], ['9', ' CA ', 384.065, 165.174, 196.093], ['9', ' C ', 385.178, 164.61, 195.204], ['9', ' O ', 386.36, 164.824, 195.476], ['9', ' CB ', 383.871, 164.274, 197.317], ['9', ' H ', 382.069, 164.712, 195.674], ['9', ' HA ', 384.35, 166.056, 196.41], ['9', ' HB2', 383.177, 164.652, 197.879], ['9', ' HB3', 383.493, 163.44, 197.05]]
[['9', ' N ', 384.789, 163.885, 194.153], ['9', ' CA ', 385.726, 163.405, 193.136], ['9', ' C ', 386.327, 164.557, 192.322], ['9', ' O ', 387.527, 164.559, 192.041], ['9', ' CB ', 385.031, 162.415, 192.196], ['9', ' H ', 383.836, 163.599, 193.981], ['9', ' HA ', 386.462, 162.932, 193.578], ['9', ' HB2', 384.708, 161.661, 192.714], ['9', ' HB3', 384.21, 162.785, 191.813]]
[['9', ' N ', 385.492, 165.527, 191.948], ['9', ' CA ', 385.943, 166.697, 191.187], ['9', ' C ', 386.687, 167.694, 192.078], ['9', ' O ', 387.534, 168.456, 191.608], ['9', ' CB ', 384.752, 167.39, 190.521], ['9', ' H ', 384.503, 165.531, 192.151], ['9', ' HA ', 386.555, 166.407, 190.479], ['9', ' HB2', 384.271, 166.742, 189.982], ['9', ' HB3', 384.037, 167.58, 191.157]]
[['9', ' N ', 383.868, 172.727, 193.773], ['9', ' CA ', 382.863, 173.472, 194.526], ['9', ' C ', 383.017, 173.232, 196.024], ['9', ' O ', 383.16, 174.178, 196.8], ['9', ' CB ', 381.457, 173.072, 194.074], ['9', ' H ', 384.677, 172.45, 194.312], ['9', ' HA ', 382.978, 174.43, 194.356], ['9', ' HB2', 381.342, 173.32, 193.144], ['9', ' HB3', 381.274, 172.127, 194.233]]
[['9', ' N ', 382.978, 171.96, 196.418], ['9', ' CA ', 383.217, 171.556, 197.806], ['9', ' C ', 384.71, 171.332, 198.07], ['9', ' O ', 385.176, 171.531, 199.191], ['9', ' CB ', 382.42, 170.294, 198.151], ['9', ' OG ', 382.742, 169.225, 197.279], ['9', ' H ', 382.785, 171.186, 195.798], ['9', ' HA ', 382.911, 172.266, 198.409], ['9', ' HB2', 382.627, 170.03, 199.061], ['9', ' HB3', 381.473, 170.489, 198.072], ['9', ' HG ', 382.243, 168.558, 197.438]]
[['9', ' N ', 385.451, 170.916, 197.04], ['9', ' CA ', 386.915, 170.815, 197.114], ['9', ' C ', 387.55, 172.198, 197.287], ['9', ' O ', 388.569, 172.345, 197.964], ['9', ' CB ', 387.474, 170.137, 195.858], ['9', ' H ', 385.074, 170.635, 196.146], ['9', ' HA ', 387.161, 170.267, 197.889], ['9', ' HB2', 387.055, 169.268, 195.755], ['9', ' HB3', 387.16, 170.638, 195.054]]
[['9', ' N ', 386.932, 173.202, 196.667], ['9', ' CA ', 387.317, 174.6, 196.83], ['9', ' C ', 386.952, 175.095, 198.222], ['9', ' O ', 387.723, 175.843, 198.83], ['9', ' CB ', 386.627, 175.505, 195.781], ['9', ' CG1', 387.067, 176.956, 195.948], ['9', ' CG2', 386.918, 175.015, 194.366], ['9', ' H ', 386.145, 173.07, 196.05], ['9', ' HA ', 388.286, 174.684, 196.717], ['9', ' HB ', 385.657, 175.468, 195.918], ['9', 'HG11', 386.554, 177.363, 196.651], ['9', 'HG12', 386.917, 177.429, 195.126], ['9', 'HG13', 388.0, 176.978, 196.17], ['9', 'HG21', 387.853, 174.81, 194.293], ['9', 'HG22', 386.684, 175.702, 193.737], ['9', 'HG23', 386.397, 174.229, 194.189]]
[['9', ' N ', 385.775, 174.683, 198.699], ['9', ' CA ', 385.277, 175.058, 200.017], ['9', ' C ', 386.256, 174.627, 201.093], ['9', ' O ', 386.568, 175.411, 202.001], ['9', ' CB ', 383.907, 174.43, 200.275], ['9', ' H ', 385.134, 174.098, 198.183], ['9', ' HA ', 385.181, 176.032, 200.061], ['9', ' HB2', 383.286, 174.735, 199.595], ['9', ' HB3', 383.98, 173.439, 200.221]]
[['9', ' N ', 386.73, 173.388, 200.966], ['9', ' CA ', 387.683, 172.81, 201.92], ['9', ' C ', 388.95, 173.659, 201.966], ['9', ' O ', 389.461, 173.976, 203.05], ['9', ' CB ', 388.041, 171.344, 201.575], ['9', ' CG1', 386.825, 170.432, 201.771], ['9', ' CG2', 389.19, 170.845, 202.446], ['9', ' CD1', 386.906, 169.123, 201.014], ['9', ' H ', 386.477, 172.763, 200.215], ['9', ' HA ', 387.281, 172.819, 202.814], ['9', ' HB ', 388.315, 171.301, 200.646], ['9', 'HG12', 386.741, 170.221, 202.714], ['9', 'HG13', 386.031, 170.892, 201.47], ['9', 'HG21', 390.023, 171.145, 202.074], ['9', 'HG22', 389.179, 169.886, 202.47], ['9', 'HG23', 389.084, 171.19, 203.336], ['9', 'HD11', 387.115, 169.307, 200.095], ['9', 'HD12', 386.058, 168.677, 201.073], ['9', 'HD13', 387.592, 168.575, 201.403]]
[['9', ' N ', 389.427, 174.013, 200.777], ['9', ' CA ', 390.634, 174.83, 200.619], ['9', ' C ', 390.457, 176.166, 201.332], ['9', ' O ', 391.35, 176.62, 202.063], ['9', ' CB ', 390.957, 175.045, 199.147], ['9', ' H ', 389.005, 173.746, 199.899], ['9', ' HA ', 391.391, 174.364, 201.031], ['9', ' HB1', 390.969, 174.195, 198.701], ['9', ' HB2', 391.818, 175.464, 199.076], ['9', ' HB3', 390.288, 175.611, 198.756]]
[['9', ' N ', 389.293, 176.767, 201.102], ['9', ' CA ', 388.933, 178.054, 201.698], ['9', ' C ', 388.982, 177.961, 203.218], ['9', ' O ', 389.541, 178.834, 203.896], ['9', ' CB ', 387.541, 178.492, 201.239], ['9', ' H ', 388.575, 176.391, 200.5], ['9', ' HA ', 389.579, 178.734, 201.411], ['9', ' HB2', 387.527, 178.537, 200.27], ['9', ' HB3', 386.878, 177.807, 201.495]]
[['9', ' N ', 388.387, 176.885, 203.725], ['9', ' CA ', 388.326, 176.609, 205.162], ['9', ' C ', 389.732, 176.529, 205.738], ['9', ' O ', 390.025, 177.119, 206.787], ['9', ' CB ', 387.577, 175.302, 205.429], ['9', ' H ', 387.928, 176.181, 203.164], ['9', ' HA ', 387.848, 177.336, 205.612], ['9', ' HB2', 386.682, 175.369, 205.059], ['9', ' HB3', 388.033, 174.556, 204.955]]
[['9', ' N ', 390.582, 175.793, 205.028], ['9', ' CA ', 391.98, 175.595, 205.413], ['9', ' C ', 392.689, 176.94, 205.518], ['9', ' O ', 393.407, 177.209, 206.494], ['9', ' CB ', 392.698, 174.701, 204.399], ['9', ' H ', 390.331, 175.309, 204.177], ['9', ' HA ', 392.016, 175.158, 206.289], ['9', ' HB2', 392.258, 173.837, 204.372], ['9', ' HB3', 392.663, 175.118, 203.5]]
[['9', ' N ', 392.465, 177.763, 204.497], ['9', ' CA ', 393.053, 179.101, 204.41], ['9', ' C ', 392.646, 179.931, 205.623], ['9', ' O ', 393.481, 180.596, 206.253], ['9', ' CB ', 392.61, 179.837, 203.131], ['9', ' H ', 391.883, 177.531, 203.705], ['9', ' HA ', 394.03, 179.026, 204.401], ['9', ' HB ', 391.618, 179.935, 203.124]]
[['9', ' N ', 391.352, 179.868, 205.925], ['9', ' CA ', 390.763, 180.595, 207.051], ['9', ' C ', 391.441, 180.18, 208.352], ['9', ' O ', 391.81, 181.026, 209.178], ['9', ' CB ', 389.261, 180.357, 207.128], ['9', ' H ', 390.679, 179.324, 205.403], ['9', ' HA ', 390.912, 181.555, 206.925], ['9', ' HB1', 388.871, 180.53, 206.267], ['9', ' HB2', 388.886, 180.952, 207.781], ['9', ' HB3', 389.098, 179.447, 207.385]]
[['9', ' N ', 391.593, 178.867, 208.502], ['9', ' CA ', 392.222, 178.269, 209.682], ['9', ' C ', 393.64, 178.803, 209.846], ['9', ' O ', 394.051, 179.19, 210.949], ['9', ' CB ', 392.245, 176.742, 209.57], ['9', ' H ', 391.284, 178.184, 207.825], ['9', ' HA ', 391.708, 178.511, 210.48], ['9', ' HB2', 391.334, 176.417, 209.494], ['9', ' HB3', 392.744, 176.48, 208.755]]
[['9', ' N ', 394.359, 178.814, 208.727], ['9', ' CA ', 395.738, 179.299, 208.676], ['9', ' C ', 395.816, 180.75, 209.155], ['9', ' O ', 396.682, 181.094, 209.97], ['9', ' CB ', 396.309, 179.165, 207.27], ['9', ' H ', 394.015, 178.487, 207.835], ['9', ' HA ', 396.288, 178.754, 209.277], ['9', ' HB1', 396.158, 178.271, 206.953], ['9', ' HB2', 397.252, 179.345, 207.301], ['9', ' HB3', 395.877, 179.796, 206.692]]
[['9', ' N ', 394.93, 181.603, 208.643], ['9', ' CA ', 394.915, 183.021, 209.012], ['9', ' C ', 394.212, 183.231, 210.349], ['9', ' O ', 394.761, 182.92, 211.406], ['9', ' CB ', 394.225, 183.851, 207.927], ['9', ' H ', 394.217, 181.347, 207.974], ['9', ' HA ', 395.835, 183.348, 209.097], ['9', ' HB2', 394.676, 183.703, 207.081], ['9', ' HB3', 393.308, 183.518, 207.751]]
Please check result here: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/daq_score_w9.pdb
Please open it in pymol and visualize it by putting the following command to Pymol:
----------------------------------------------------------------------------------------------------
spectrum b, red_white_blue, all, -1,1
----------------------------------------------------------------------------------------------------
INFO : STEP-0 DAQ Done
INFO: leave DAQ dir, enter DAQ_refine
INFO: STEP-1: Running strategy 1
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
'S1_results' folder has been removed.
'S2_results' folder has been removed.
'Vanilla_AF2_results' folder has been removed.
'DAQ' folder has been removed.
'template' folder has been removed.
Deleted: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/prediction.txt
Deleted: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/9d089ca034a9340fc99ca25a77b27bc2_b03c7.custom.a3m
Deleted: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/9d089ca034a9340fc99ca25a77b27bc2_b03c7.csv
Deleted: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/9d089ca034a9340fc99ca25a77b27bc2_d5def.csv
Deleted: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/9d089ca034a9340fc99ca25a77b27bc2_07378.csv
INFO: Input Protein Sequence and DAQ result file started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Prepare trimmed template finished.
MSA finished.(if applicable)
INFO: Input Protein Sequence and DAQ result file Done
INFO: Modeling Part started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
MSA settings finished.
Advanced settings finished.
Current working directory set to /bio/kihara-web/www/em/emweb-jobscheduler/algorithms/DAQ-Refine
Install dependencies finished.
GPU is available!
GPU Name: NVIDIA GeForce RTX 2080 Ti
Total Memory: 11019.4375 MB
Allocated Memory: 0.0 MB
Cached Memory: 0.0 MB
Free Memory: 11019.4375 MB
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
2023-11-13 05:17:25,463 Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: Interpreter CUDA
2023-11-13 05:17:25,467 Unable to initialize backend 'tpu': module 'jaxlib.xla_extension' has no attribute 'get_tpu_client'
2023-11-13 05:17:34,303 Running on GPU
2023-11-13 05:17:34,717 Found 7 citations for tools or databases
2023-11-13 05:17:34,785 Adding missing field revision_date to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2/chain_9/template/1tmp.cif. Backing up original file to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2/chain_9/template/1tmp.cif.bak.
2023-11-13 05:17:34,894 Query 1/1: 9d089ca034a9340fc99ca25a77b27bc2_07378 (length 253)
2023-11-13 05:17:37,473 Sequence 0 found templates: ['1tmp_9']
2023-11-13 05:17:37,555 Setting max_seq=512, max_extra_seq=620
2023-11-13 05:18:20,113 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=81.6 pTM=0.748
2023-11-13 05:18:29,003 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=81.2 pTM=0.752 tol=2.57
2023-11-13 05:18:29,013 alphafold2_ptm_model_1_seed_000 took 43.6s (1 recycles)
2023-11-13 05:18:37,997 alphafold2_ptm_model_2_seed_000 recycle=0 pLDDT=83.9 pTM=0.77
2023-11-13 05:18:46,933 alphafold2_ptm_model_2_seed_000 recycle=1 pLDDT=83.6 pTM=0.777 tol=7.01
2023-11-13 05:18:46,933 alphafold2_ptm_model_2_seed_000 took 17.8s (1 recycles)
2023-11-13 05:19:11,038 alphafold2_ptm_model_3_seed_000 recycle=0 pLDDT=83.6 pTM=0.767
2023-11-13 05:19:19,721 alphafold2_ptm_model_3_seed_000 recycle=1 pLDDT=85.1 pTM=0.782 tol=1.29
2023-11-13 05:19:19,722 alphafold2_ptm_model_3_seed_000 took 32.7s (1 recycles)
2023-11-13 05:19:28,485 alphafold2_ptm_model_4_seed_000 recycle=0 pLDDT=81.6 pTM=0.755
2023-11-13 05:19:37,199 alphafold2_ptm_model_4_seed_000 recycle=1 pLDDT=85.4 pTM=0.783 tol=1.79
2023-11-13 05:19:37,200 alphafold2_ptm_model_4_seed_000 took 17.4s (1 recycles)
2023-11-13 05:19:46,042 alphafold2_ptm_model_5_seed_000 recycle=0 pLDDT=83.4 pTM=0.768
2023-11-13 05:19:54,796 alphafold2_ptm_model_5_seed_000 recycle=1 pLDDT=85.9 pTM=0.795 tol=1.03
2023-11-13 05:19:54,796 alphafold2_ptm_model_5_seed_000 took 17.5s (1 recycles)
2023-11-13 05:19:55,312 reranking models by 'plddt' metric
2023-11-13 05:19:55,313 rank_001_alphafold2_ptm_model_5_seed_000 pLDDT=85.9 pTM=0.795
2023-11-13 05:19:55,316 rank_002_alphafold2_ptm_model_4_seed_000 pLDDT=85.4 pTM=0.783
2023-11-13 05:19:55,319 rank_003_alphafold2_ptm_model_3_seed_000 pLDDT=85.1 pTM=0.782
2023-11-13 05:19:55,324 rank_004_alphafold2_ptm_model_2_seed_000 pLDDT=83.6 pTM=0.777
2023-11-13 05:19:55,327 rank_005_alphafold2_ptm_model_1_seed_000 pLDDT=81.2 pTM=0.752
2023-11-13 05:19:57,352 Done
Prediction finished.
INFO: Modeling Part Done
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_001_alphafold2_ptm_model_5_seed_000_s1
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=2109425458 seed_offset=0 real_seed=2109425458
core.init.random: RandomGenerator:init: Normal mode, seed=2109425458 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.81 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.15 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 178.247 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5211 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12642928 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3647.99 0.667664 0.667664 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4605 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9963420 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3592.77 0.732467 0.732467 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4451 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9281084 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3539.83 0.749275 0.749275 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4336 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8799372 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3483.14 0.758073 0.758073 0.55
protocols.relax.FastRelax: MRP: 0 -3483.14 -3483.14 0.758073 0.758073
protocols.relax.FastRelax: CMD: accept_to_best -3483.14 0.758073 0.758073 0.55
protocols.relax.FastRelax: CMD: endrepeat -3483.14 0.758073 0.758073 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5220 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12450240 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3718.89 0.851613 0.851613 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4569 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9980232 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3615.98 0.828295 0.828295 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4421 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9266832 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3555.41 0.826729 0.826729 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4337 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8774604 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3493.07 0.822758 0.822758 0.55
protocols.relax.FastRelax: MRP: 1 -3493.07 -3493.07 0.822758 0.822758
protocols.relax.FastRelax: CMD: accept_to_best -3493.07 0.822758 0.822758 0.55
protocols.relax.FastRelax: CMD: endrepeat -3493.07 0.822758 0.822758 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 190 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 190 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_002_alphafold2_ptm_model_4_seed_000_s1
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-871634679 seed_offset=0 real_seed=-871634679
core.init.random: RandomGenerator:init: Normal mode, seed=-871634679 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.74 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -610.262 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5221 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12473304 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3479.05 0.680607 0.680607 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4552 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9677580 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3429.28 0.750173 0.750173 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4457 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9178396 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3391.91 0.813171 0.813171 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4338 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8679052 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3342.14 0.860588 0.860588 0.55
protocols.relax.FastRelax: MRP: 0 -3342.14 -3342.14 0.860588 0.860588
protocols.relax.FastRelax: CMD: accept_to_best -3342.14 0.860588 0.860588 0.55
protocols.relax.FastRelax: CMD: endrepeat -3342.14 0.860588 0.860588 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5225 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12420976 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3575.31 0.956896 0.956896 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4639 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9958608 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3475.99 0.949294 0.949294 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4434 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9175584 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3417.41 0.94993 0.94993 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4303 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8612916 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3356.86 0.953281 0.953281 0.55
protocols.relax.FastRelax: MRP: 1 -3356.86 -3356.86 0.953281 0.953281
protocols.relax.FastRelax: CMD: accept_to_best -3356.86 0.953281 0.953281 0.55
protocols.relax.FastRelax: CMD: endrepeat -3356.86 0.953281 0.953281 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 188 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 188 seconds

Align structures finished.
====================================================================Modeling finished====================================================================
Selected strategy mode: strategy 1
Input query sequence: MENSMMFISRSLRRPVTALNCNLQSVRTVIYLHKGPRINGLRRDPESYLRNPSGVLFTEVNAKECQDKVRSILQLPKYGINLSNELILQCLTHKSFAHGSKPYNEKLNLLGAQFLKLQTCIHSLKNGSPAESCENGQLSLQFSNLGTKFAKELTSKNTACTFVKLHNLGPFIFWKMRDPIKDGHINGETTIFASVLNAFIGAILSTNGSEKAAKFIQGSLLDKEDLHSLVNIANENVASAKAKISDKENKAFL
Job ID: 9d089ca034a9340fc99ca25a77b27bc2_07378
Number of models to use: 0
Template mode: custom
Output directory: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ
====================================================================Modeling finished====================================================================
INFO: STEP-2: Running Vanilla AF2
INFO: Input Protein Sequence and DAQ result file started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Prepare trimmed template finished.
MSA finished.(if applicable)
INFO: Input Protein Sequence and DAQ result file Done
INFO: Modeling Part started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
MSA settings finished.
Advanced settings finished.
Current working directory set to /bio/kihara-web/www/em/emweb-jobscheduler/algorithms/DAQ-Refine
Install dependencies finished.
GPU is available!
GPU Name: NVIDIA GeForce RTX 2080 Ti
Total Memory: 11019.4375 MB
Allocated Memory: 0.0 MB
Cached Memory: 0.0 MB
Free Memory: 11019.4375 MB
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Prediction finished.
INFO: Modeling Part Done
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_001_alphafold2_ptm_model_5_seed_000_af2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1098735251 seed_offset=0 real_seed=1098735251
core.init.random: RandomGenerator:init: Normal mode, seed=1098735251 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.73 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 141.355 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5226 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12691596 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3684.33 0.7609 0.7609 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4601 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9915996 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3629.56 0.90361 0.90361 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4514 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9391640 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3594.1 1.07197 1.07197 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4366 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8783124 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3549.82 1.2291 1.2291 0.55
protocols.relax.FastRelax: MRP: 0 -3549.82 -3549.82 1.2291 1.2291
protocols.relax.FastRelax: CMD: accept_to_best -3549.82 1.2291 1.2291 0.55
protocols.relax.FastRelax: CMD: endrepeat -3549.82 1.2291 1.2291 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5221 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12371252 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3795.47 1.32247 1.32247 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4596 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9979088 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3691.27 1.37536 1.37536 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4464 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9299564 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3631.47 1.46592 1.46592 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4322 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8738280 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3569.5 1.49419 1.49419 0.55
protocols.relax.FastRelax: MRP: 1 -3569.5 -3569.5 1.49419 1.49419
protocols.relax.FastRelax: CMD: accept_to_best -3569.5 1.49419 1.49419 0.55
protocols.relax.FastRelax: CMD: endrepeat -3569.5 1.49419 1.49419 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 189 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 189 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_002_alphafold2_ptm_model_3_seed_000_af2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-322978997 seed_offset=0 real_seed=-322978997
core.init.random: RandomGenerator:init: Normal mode, seed=-322978997 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.95 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -812.521 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5224 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12817716 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3679.98 0.578616 0.578616 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4546 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10158060 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3613.99 0.624911 0.624911 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4459 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9602432 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3562.36 0.641097 0.641097 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4321 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9039896 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3500.15 0.64707 0.64707 0.55
protocols.relax.FastRelax: MRP: 0 -3500.15 -3500.15 0.64707 0.64707
protocols.relax.FastRelax: CMD: accept_to_best -3500.15 0.64707 0.64707 0.55
protocols.relax.FastRelax: CMD: endrepeat -3500.15 0.64707 0.64707 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5247 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 13044436 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3754.85 0.772905 0.772905 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4624 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10403636 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3645.07 0.760149 0.760149 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4490 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9803104 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3583.79 0.765045 0.765045 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4332 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9072620 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3520.56 0.769051 0.769051 0.55
protocols.relax.FastRelax: MRP: 1 -3520.56 -3520.56 0.769051 0.769051
protocols.relax.FastRelax: CMD: accept_to_best -3520.56 0.769051 0.769051 0.55
protocols.relax.FastRelax: CMD: endrepeat -3520.56 0.769051 0.769051 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 191 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 191 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_003_alphafold2_ptm_model_4_seed_000_af2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=2015440157 seed_offset=0 real_seed=2015440157
core.init.random: RandomGenerator:init: Normal mode, seed=2015440157 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.76 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -673.435 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5226 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12529228 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3601.84 0.607197 0.607197 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4591 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9920312 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3536.1 0.656171 0.656171 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4472 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9311940 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3484.84 0.678998 0.678998 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4375 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8827564 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3433.72 0.718894 0.718894 0.55
protocols.relax.FastRelax: MRP: 0 -3433.72 -3433.72 0.718894 0.718894
protocols.relax.FastRelax: CMD: accept_to_best -3433.72 0.718894 0.718894 0.55
protocols.relax.FastRelax: CMD: endrepeat -3433.72 0.718894 0.718894 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5262 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12576268 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3673.37 0.809064 0.809064 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4630 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9960208 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3566.61 0.782402 0.782402 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4471 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9233324 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3509.47 0.779735 0.779735 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4375 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8783956 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3448.82 0.780678 0.780678 0.55
protocols.relax.FastRelax: MRP: 1 -3448.82 -3448.82 0.780678 0.780678
protocols.relax.FastRelax: CMD: accept_to_best -3448.82 0.780678 0.780678 0.55
protocols.relax.FastRelax: CMD: endrepeat -3448.82 0.780678 0.780678 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 190 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 190 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_004_alphafold2_ptm_model_2_seed_000_af2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=160977332 seed_offset=0 real_seed=160977332
core.init.random: RandomGenerator:init: Normal mode, seed=160977332 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.76 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -638.719 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5189 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12680628 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3645.98 0.620497 0.620497 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4614 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10184440 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3575.8 0.679261 0.679261 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4461 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9528800 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3526.98 0.715254 0.715254 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4358 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8993220 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3468.6 0.746468 0.746468 0.55
protocols.relax.FastRelax: MRP: 0 -3468.6 -3468.6 0.746468 0.746468
protocols.relax.FastRelax: CMD: accept_to_best -3468.6 0.746468 0.746468 0.55
protocols.relax.FastRelax: CMD: endrepeat -3468.6 0.746468 0.746468 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5218 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12693104 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3714.58 0.854157 0.854157 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4600 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10084884 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3611.13 0.848257 0.848257 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4455 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9440620 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3553.57 0.881631 0.881631 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4345 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8960276 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3493.48 0.916288 0.916288 0.55
protocols.relax.FastRelax: MRP: 1 -3493.48 -3493.48 0.916288 0.916288
protocols.relax.FastRelax: CMD: accept_to_best -3493.48 0.916288 0.916288 0.55
protocols.relax.FastRelax: CMD: endrepeat -3493.48 0.916288 0.916288 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 190 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 190 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_005_alphafold2_ptm_model_1_seed_000_af2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1870103389 seed_offset=0 real_seed=-1870103389
core.init.random: RandomGenerator:init: Normal mode, seed=-1870103389 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.87 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -866.351 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5197 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12879856 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3624.33 0.603759 0.603759 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4638 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10390400 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3571.96 0.69793 0.69793 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4563 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9918776 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3528.37 0.76844 0.76844 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4390 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9248988 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3477.53 0.858459 0.858459 0.55
protocols.relax.FastRelax: MRP: 0 -3477.53 -3477.53 0.858459 0.858459
protocols.relax.FastRelax: CMD: accept_to_best -3477.53 0.858459 0.858459 0.55
protocols.relax.FastRelax: CMD: endrepeat -3477.53 0.858459 0.858459 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5242 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12927760 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3724.66 0.976738 0.976738 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4634 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 10390784 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3607.75 0.956495 0.956495 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4476 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9746996 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3547.09 0.96279 0.96279 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4350 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9216440 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3484.91 0.969061 0.969061 0.55
protocols.relax.FastRelax: MRP: 1 -3484.91 -3484.91 0.969061 0.969061
protocols.relax.FastRelax: CMD: accept_to_best -3484.91 0.969061 0.969061 0.55
protocols.relax.FastRelax: CMD: endrepeat -3484.91 0.969061 0.969061 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 190 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 190 seconds

Align structures finished.
====================================================================Modeling finished====================================================================
Selected strategy mode: Vanilla AF2
Input query sequence: MENSMMFISRSLRRPVTALNCNLQSVRTVIYLHKGPRINGLRRDPESYLRNPSGVLFTEVNAKECQDKVRSILQLPKYGINLSNELILQCLTHKSFAHGSKPYNEKLNLLGAQFLKLQTCIHSLKNGSPAESCENGQLSLQFSNLGTKFAKELTSKNTACTFVKLHNLGPFIFWKMRDPIKDGHINGETTIFASVLNAFIGAILSTNGSEKAAKFIQGSLLDKEDLHSLVNIANENVASAKAKISDKENKAFL
Job ID: 9d089ca034a9340fc99ca25a77b27bc2_30f58
Number of models to use: 0
Template mode: none
Output directory: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ
====================================================================Modeling finished====================================================================
STEP-3: Running strategy 2
INFO: Input Protein Sequence and DAQ result file started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Prepare trimmed template finished.
MSA finished.(if applicable)
INFO: Input Protein Sequence and DAQ result file Done
INFO: Modeling Part started
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
moving /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/trimmed_msa.a3m to 9d089ca034a9340fc99ca25a77b27bc2_ed49f.custom.a3m
The size of '9d089ca034a9340fc99ca25a77b27bc2_ed49f.custom.a3m' is 355347 bytes.
MSA settings finished.
Advanced settings finished.
Current working directory set to /bio/kihara-web/www/em/emweb-jobscheduler/algorithms/DAQ-Refine
Install dependencies finished.
GPU is available!
GPU Name: NVIDIA GeForce RTX 2080 Ti
Total Memory: 11019.4375 MB
Allocated Memory: 0.0 MB
Cached Memory: 0.0 MB
Free Memory: 11019.4375 MB
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
2023-11-13 05:45:02,112 Running on GPU
2023-11-13 05:45:02,122 Found 4 citations for tools or databases
2023-11-13 05:45:02,190 Adding missing field revision_date to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2/chain_9/template/1tmp.cif. Backing up original file to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2/chain_9/template/1tmp.cif.bak.
2023-11-13 05:45:02,486 Query 1/1: 9d089ca034a9340fc99ca25a77b27bc2_ed49f.custom (length 253)
2023-11-13 05:45:03,155 Sequence 0 found templates: ['1tmp_9', '1tmp_9']
2023-11-13 05:45:03,281 Setting max_seq=512, max_extra_seq=620
2023-11-13 05:45:39,206 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=84.2 pTM=0.735
2023-11-13 05:45:48,028 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=74.6 pTM=0.675 tol=2.2
2023-11-13 05:45:48,029 alphafold2_ptm_model_1_seed_000 took 40.6s (1 recycles)
2023-11-13 05:45:57,012 alphafold2_ptm_model_2_seed_000 recycle=0 pLDDT=83.2 pTM=0.73
2023-11-13 05:46:05,901 alphafold2_ptm_model_2_seed_000 recycle=1 pLDDT=78.5 pTM=0.7 tol=2.87
2023-11-13 05:46:05,901 alphafold2_ptm_model_2_seed_000 took 17.8s (1 recycles)
2023-11-13 05:46:29,306 alphafold2_ptm_model_3_seed_000 recycle=0 pLDDT=45 pTM=0.21
2023-11-13 05:46:37,925 alphafold2_ptm_model_3_seed_000 recycle=1 pLDDT=50.5 pTM=0.246 tol=11.1
2023-11-13 05:46:37,925 alphafold2_ptm_model_3_seed_000 took 31.8s (1 recycles)
2023-11-13 05:46:46,676 alphafold2_ptm_model_4_seed_000 recycle=0 pLDDT=44.6 pTM=0.239
2023-11-13 05:46:55,347 alphafold2_ptm_model_4_seed_000 recycle=1 pLDDT=38.2 pTM=0.194 tol=17.2
2023-11-13 05:46:55,348 alphafold2_ptm_model_4_seed_000 took 17.3s (1 recycles)
2023-11-13 05:47:04,139 alphafold2_ptm_model_5_seed_000 recycle=0 pLDDT=44.2 pTM=0.201
2023-11-13 05:47:12,848 alphafold2_ptm_model_5_seed_000 recycle=1 pLDDT=47.3 pTM=0.223 tol=14.2
2023-11-13 05:47:12,848 alphafold2_ptm_model_5_seed_000 took 17.4s (1 recycles)
2023-11-13 05:47:12,940 reranking models by 'plddt' metric
2023-11-13 05:47:12,942 rank_001_alphafold2_ptm_model_2_seed_000 pLDDT=78.5 pTM=0.7
2023-11-13 05:47:12,944 rank_002_alphafold2_ptm_model_1_seed_000 pLDDT=74.6 pTM=0.675
2023-11-13 05:47:12,946 rank_003_alphafold2_ptm_model_3_seed_000 pLDDT=50.5 pTM=0.246
2023-11-13 05:47:12,948 rank_004_alphafold2_ptm_model_5_seed_000 pLDDT=47.3 pTM=0.223
2023-11-13 05:47:12,950 rank_005_alphafold2_ptm_model_4_seed_000 pLDDT=38.2 pTM=0.194
2023-11-13 05:47:14,946 Done
Prediction finished.
INFO: Modeling Part Done
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_001_alphafold2_ptm_model_2_seed_000_s2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=745495758 seed_offset=0 real_seed=745495758
core.init.random: RandomGenerator:init: Normal mode, seed=745495758 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.71 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.15 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat -19.8433 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5107 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 11350500 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3259.68 0.732825 0.732825 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4640 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9609760 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3262.35 1.07022 1.07022 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4478 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8751728 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3243.52 1.32465 1.32465 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4396 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8415424 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3207.42 1.4639 1.4639 0.55
protocols.relax.FastRelax: MRP: 0 -3207.42 -3207.42 1.4639 1.4639
protocols.relax.FastRelax: CMD: accept_to_best -3207.42 1.4639 1.4639 0.55
protocols.relax.FastRelax: CMD: endrepeat -3207.42 1.4639 1.4639 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5254 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12030404 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3461.8 1.5913 1.5913 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4647 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9662544 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3354.06 1.61153 1.61153 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4436 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8731520 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3292.35 1.64459 1.64459 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4291 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8136596 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3229.47 1.67658 1.67658 0.55
protocols.relax.FastRelax: MRP: 1 -3229.47 -3229.47 1.67658 1.67658
protocols.relax.FastRelax: CMD: accept_to_best -3229.47 1.67658 1.67658 0.55
protocols.relax.FastRelax: CMD: endrepeat -3229.47 1.67658 1.67658 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 184 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 184 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_002_alphafold2_ptm_model_1_seed_000_s2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=284604492 seed_offset=0 real_seed=284604492
core.init.random: RandomGenerator:init: Normal mode, seed=284604492 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.82 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.15 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 945.487 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5053 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 11787604 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3108.98 0.686648 0.686648 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4586 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9776276 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3114.68 0.856081 0.856081 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4443 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9101640 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3096.38 1.01272 1.01272 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4277 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8541940 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3045.87 1.18335 1.18335 0.55
protocols.relax.FastRelax: MRP: 0 -3045.87 -3045.87 1.18335 1.18335
protocols.relax.FastRelax: CMD: accept_to_best -3045.87 1.18335 1.18335 0.55
protocols.relax.FastRelax: CMD: endrepeat -3045.87 1.18335 1.18335 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 5227 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 12242220 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3320.48 1.32972 1.32972 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4588 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9999248 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3210.92 1.34511 1.34511 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4437 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 9079844 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3158.88 1.448 1.448 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4334 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 8602528 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -3102.21 1.56147 1.56147 0.55
protocols.relax.FastRelax: MRP: 1 -3102.21 -3102.21 1.56147 1.56147
protocols.relax.FastRelax: CMD: accept_to_best -3102.21 1.56147 1.56147 0.55
protocols.relax.FastRelax: CMD: endrepeat -3102.21 1.56147 1.56147 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 186 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 186 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_003_alphafold2_ptm_model_3_seed_000_s2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-2113857111 seed_offset=0 real_seed=-2113857111
core.init.random: RandomGenerator:init: Normal mode, seed=-2113857111 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.86 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 8076.92 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4349 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3348780 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min 599.72 1.05621 1.05621 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4579 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3596144 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min 300.233 1.95689 1.95689 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4535 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3756600 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min 131.655 2.62447 2.62447 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4433 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3727952 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min 77.2285 3.03044 3.03044 0.55
protocols.relax.FastRelax: MRP: 0 77.2285 77.2285 3.03044 3.03044
protocols.relax.FastRelax: CMD: accept_to_best 77.2285 3.03044 3.03044 0.55
protocols.relax.FastRelax: CMD: endrepeat 77.2285 3.03044 3.03044 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4728 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4296800 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -262.888 3.53135 3.53135 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4433 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4105404 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -224.25 3.79152 3.79152 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4368 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4017236 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -236.898 4.08178 4.08178 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4343 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3997468 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -239.667 4.23546 4.23546 0.55
protocols.relax.FastRelax: MRP: 1 -239.667 -239.667 4.23546 4.23546
protocols.relax.FastRelax: CMD: accept_to_best -239.667 4.23546 4.23546 0.55
protocols.relax.FastRelax: CMD: endrepeat -239.667 4.23546 4.23546 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 139 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 139 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_004_alphafold2_ptm_model_5_seed_000_s2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-899116703 seed_offset=0 real_seed=-899116703
core.init.random: RandomGenerator:init: Normal mode, seed=-899116703 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.89 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.14 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 6756.75 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4503 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3266444 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -313.979 1.11353 1.11353 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4571 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3335856 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -514.379 1.93028 1.93028 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4528 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3307164 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -616.098 2.60252 2.60252 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4530 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3348000 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -713.079 3.06129 3.06129 0.55
protocols.relax.FastRelax: MRP: 0 -713.079 -713.079 3.06129 3.06129
protocols.relax.FastRelax: CMD: accept_to_best -713.079 3.06129 3.06129 0.55
protocols.relax.FastRelax: CMD: endrepeat -713.079 3.06129 3.06129 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4851 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3814932 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -990.292 3.5145 3.5145 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4577 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3559768 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -987.941 3.89939 3.89939 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4540 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3549372 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -1040.11 4.17644 4.17644 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4472 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3444924 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -1039.23 4.41276 4.41276 0.55
protocols.relax.FastRelax: MRP: 1 -1039.23 -1039.23 4.41276 4.41276
protocols.relax.FastRelax: CMD: accept_to_best -1039.23 4.41276 4.41276 0.55
protocols.relax.FastRelax: CMD: endrepeat -1039.23 4.41276 4.41276 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 137 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 137 seconds

Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9
align structure to input map
Current working directory set to /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_005_alphafold2_ptm_model_4_seed_000_s2
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but -weights are also specified. Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
core.init: command: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/ -in::file::s input.pdb -parser::protocol B_relax_density.xml -ignore_unrecognized_res -edensity::mapreso 3.43 -edensity::cryoem_scatterers -crystal_refine -beta -out::suffix _relax -default_max_cycles 200
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1392419418 seed_offset=0 real_seed=1392419418
core.init.random: RandomGenerator:init: Normal mode, seed=1392419418 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed input.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB input.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.91 seconds.
core.import_pose.import_pose: File 'input.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density.xml
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="dens" weights="beta_cart">
<Reweight scoretype="elec_dens_fast" weight="35.0"/>
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</ScoreFunction>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name="setupdens"/>
<LoadDensityMap mapfile="MAP.mrc" name="loaddens"/>
<FastRelax cartesian="1" name="relaxcart" repeats="2" scorefxn="dens"/>
</MOVERS>
<PROTOCOLS>
<Add mover="setupdens"/>
<Add mover="loaddens"/>
<Add mover="relaxcart"/>
</PROTOCOLS>
<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 228 torsion parameters corresponding to 131380 unique torsions.
core.scoring.GenericBondedPotential: Added total 49 improper parameters corresponding to 65 unique impropers.
core.scoring.GenericBondedPotential: Added total 3 special-torsion parameters corresponding to 4 unique torsions.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2197 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader: setting dens weight elec_dens_fast to 35
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing:
protocols.jd2.parser.ScoreFunctionLoader: ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader: CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader: GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader: PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLY 1
protocols.jd2.parser.ScoreFunctionLoader: HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader: ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader: LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader: LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader: MET 0.76
protocols.jd2.parser.ScoreFunctionLoader: ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader: PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader: GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader: ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader: SER 0.81
protocols.jd2.parser.ScoreFunctionLoader: THR 0.81
protocols.jd2.parser.ScoreFunctionLoader: VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader: TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader: TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 5
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.relax.FastRelax: ================== Reading script file: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/sampling/relax_scripts/default.txt ==================
protocols.relax.FastRelax: repeat 2
protocols.relax.FastRelax: ramp_repack_min 0.02 0.01 1.0
protocols.relax.FastRelax: ramp_repack_min 0.250 0.01 0.5
protocols.relax.FastRelax: ramp_repack_min 0.550 0.01 0.0
protocols.relax.FastRelax: ramp_repack_min 1 0.00001 0.0
protocols.relax.FastRelax: accept_to_best
protocols.relax.FastRelax: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMAP.mrc
core.scoring.electron_density.ElectronDensity: Setting resolution to 3.43A
core.scoring.electron_density.ElectronDensity: atom mask to 3.2A
core.scoring.electron_density.ElectronDensity: CA mask to 6A
core.scoring.electron_density.ElectronDensity: Read density map'MAP.mrc'
core.scoring.electron_density.ElectronDensity: extent: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity: altorigin: 356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: grid: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: celldim: 46 x 69 x 62
core.scoring.electron_density.ElectronDensity: cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity: voxel vol.: 1
core.scoring.electron_density.ElectronDensity: Using ALTERNATE origin
origin =356.44 x 155.44 x 159.46
core.scoring.electron_density.ElectronDensity: Effective resolution = 3.43
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (254)
core.scoring.GenericBondedEnergy: Creating new peptide-bonded energy container (254)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1: B(C/N/O/S)=18.6329 / 22.9217 / 26.355 / 18.845 sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/kihara/gterashi/bin/rosetta_bin_linux_2018.33.60351_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.15 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat 6826.86 0 0 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4552 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3739016 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -46.5231 0.950192 0.950192 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4654 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3899200 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -254.814 1.52121 1.52121 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4474 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3755228 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -326.938 2.0349 2.0349 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4531 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 3895192 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -357.162 2.38706 2.38706 0.55
protocols.relax.FastRelax: MRP: 0 -357.162 -357.162 2.38706 2.38706
protocols.relax.FastRelax: CMD: accept_to_best -357.162 2.38706 2.38706 0.55
protocols.relax.FastRelax: CMD: endrepeat -357.162 2.38706 2.38706 0.55
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4813 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4454648 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -618.269 2.6793 2.6793 0.011
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4571 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4183864 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -550.632 2.86288 2.86288 0.1375
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4460 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4021416 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -566.169 3.37709 3.37709 0.3025
core.pack.task: Packer task: initialize from command line()
core.pack.pack_rotamers: built 4439 rotamers at 254 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 4074312 bytes
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
protocols.relax.FastRelax: CMD: ramp_repack_min -586.982 3.58356 3.58356 0.55
protocols.relax.FastRelax: MRP: 1 -586.982 -586.982 3.58356 3.58356
protocols.relax.FastRelax: CMD: accept_to_best -586.982 3.58356 3.58356 0.55
protocols.relax.FastRelax: CMD: endrepeat -586.982 3.58356 3.58356 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: input_relax_0001 reported success in 140 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 140 seconds

Align structures finished.
====================================================================Modeling finished====================================================================
Selected strategy mode: strategy 2
Input query sequence: MENSMMFISRSLRRPVTALNCNLQSVRTVIYLHKGPRINGLRRDPESYLRNPSGVLFTEVNAKECQDKVRSILQLPKYGINLSNELILQCLTHKSFAHGSKPYNEKLNLLGAQFLKLQTCIHSLKNGSPAESCENGQLSLQFSNLGTKFAKELTSKNTACTFVKLHNLGPFIFWKMRDPIKDGHINGETTIFASVLNAFIGAILSTNGSEKAAKFIQGSLLDKEDLHSLVNIANENVASAKAKISDKENKAFL
Job ID: 9d089ca034a9340fc99ca25a77b27bc2_ed49f
Number of models to use: 0
Template mode: custom
Output directory: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ
====================================================================Modeling finished====================================================================
INFO: STEP-4 Computer refined DAQ Started
gcc -O3 -c chkcmdline.c
gcc -O3 -c mrc.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -O3 -c readpdb.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -o TrimMapAtom main.c chkcmdline.o mrc.o readpdb.o -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
/net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_005_alphafold2_ptm_model_4_seed_000_s2 existed
Origin: (356.44003, 155.44, 159.46)
Previous voxel size: 1.0
----------------------------------------------------------------------------------------------------
resizing finished!
----------------------------------------------------------------------------------------------------
Finished processing model input!
0 batch processing time 0.708376
1 batch processing time 0.688223
2 batch processing time 0.695709
3 batch processing time 0.687713
4 batch processing time 0.693561
5 batch processing time 0.703648
6 batch processing time 0.693681
7 batch processing time 0.689892
8 batch processing time 0.692441
9 batch processing time 0.684869
10 batch processing time 0.686848
11 batch processing time 0.690700
12 batch processing time 0.690617
Our predictions are saved in /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_005_alphafold2_ptm_model_4_seed_000_s2/prediction.txt, please have a check!
total different chains: {'A'}
[['A', ' N ', 398.103, 161.017, 268.105], ['A', ' CA ', 398.823, 162.077, 268.791], ['A', ' C ', 398.368, 163.396, 268.245], ['A', ' O ', 398.696, 164.451, 268.782], ['A', ' CB ', 400.32, 161.928, 268.592], ['A', ' CG ', 400.937, 160.708, 269.233], ['A', ' SD ', 402.707, 160.53, 268.858], ['A', ' CE ', 403.456, 161.894, 269.76], ['A', ' H ', 397.467, 161.293, 267.371], ['A', ' HA ', 398.589, 162.042, 269.858], ['A', '1HB ', 400.526, 161.858, 267.53], ['A', '2HB ', 400.814, 162.813, 268.962], ['A', '1HG ', 400.815, 160.77, 270.312], ['A', '2HG ', 400.416, 159.819, 268.881], ['A', '1HE ', 404.536, 161.875, 269.612], ['A', '2HE ', 403.065, 162.843, 269.399], ['A', '3HE ', 403.237, 161.793, 270.824]]
[['A', ' N ', 397.628, 163.313, 267.144], ['A', ' CA ', 397.099, 164.49, 266.437], ['A', ' C ', 398.214, 165.501, 266.138], ['A', ' O ', 398.042, 166.708, 266.301], ['A', ' CB ', 395.971, 165.169, 267.243], ['A', ' CG ', 394.745, 164.28, 267.509], ['A', ' CD ', 393.576, 165.011, 268.172], ['A', ' OE1', 393.726, 166.151, 268.542], ['A', ' OE2', 392.533, 164.411, 268.297], ['A', ' H ', 397.434, 162.38, 266.805], ['A', ' HA ', 396.681, 164.162, 265.485], ['A', '1HB ', 396.355, 165.504, 268.206], ['A', '2HB ', 395.621, 166.053, 266.709], ['A', '1HG ', 394.406, 163.86, 266.563], ['A', '2HG ', 395.051, 163.455, 268.149]]
[['A', ' N ', 399.346, 164.994, 265.652], ['A', ' CA ', 400.521, 165.789, 265.341], ['A', ' C ', 400.885, 165.812, 263.855], ['A', ' O ', 402.045, 166.035, 263.501], ['A', ' CB ', 401.661, 165.259, 266.182], ['A', ' CG ', 401.924, 163.824, 265.862], ['A', ' OD1', 401.048, 163.167, 265.26], ['A', ' ND2', 403.07, 163.319, 266.24], ['A', ' H ', 399.421, 163.988, 265.527], ['A', ' HA ', 400.32, 166.818, 265.639], ['A', '1HB ', 402.563, 165.842, 266.004], ['A', '2HB ', 401.408, 165.346, 267.244], ['A', '1HD2', 403.286, 162.361, 266.04], ['A', '2HD2', 403.733, 163.889, 266.723]]
[['A', ' N ', 399.891, 165.593, 262.996], ['A', ' CA ', 400.079, 165.561, 261.545], ['A', ' C ', 398.761, 165.67, 260.781], ['A', ' O ', 398.137, 164.605, 260.683], ['A', ' CB ', 400.8, 164.305, 261.119], ['A', ' OG ', 401.052, 164.332, 259.739], ['A', ' H ', 398.974, 165.421, 263.371], ['A', ' HA ', 400.694, 166.423, 261.266], ['A', '1HB ', 401.743, 164.215, 261.662], ['A', '2HB ', 400.197, 163.432, 261.37], ['A', ' HG ', 401.49, 163.508, 259.538]]
[['A', ' N ', 398.066, 166.749, 261.135], ['A', ' CA ', 397.31, 167.423, 260.089], ['A', ' C ', 398.138, 168.452, 259.324], ['A', ' O ', 398.923, 169.2, 259.909], ['A', ' CB ', 396.066, 168.072, 260.713], ['A', ' CG ', 395.16, 168.824, 259.75], ['A', ' SD ', 394.408, 167.797, 258.508], ['A', ' CE ', 393.827, 169.098, 257.446], ['A', ' H ', 397.527, 166.644, 261.974], ['A', ' HA ', 396.981, 166.665, 259.372], ['A', '1HB ', 395.465, 167.304, 261.199], ['A', '2HB ', 396.376, 168.778, 261.486], ['A', '1HG ', 394.362, 169.3, 260.319], ['A', '2HG ', 395.718, 169.608, 259.251], ['A', '1HE ', 393.329, 168.672, 256.58], ['A', '2HE ', 393.131, 169.721, 257.994], ['A', '3HE ', 394.664, 169.707, 257.121]]
[['A', ' N ', 397.934, 168.496, 258.01], ['A', ' CA ', 398.578, 169.468, 257.15], ['A', ' C ', 397.523, 170.116, 256.274], ['A', ' O ', 396.668, 169.429, 255.721], ['A', ' CB ', 399.662, 168.783, 256.32], ['A', ' CG ', 400.443, 169.693, 255.372], ['A', ' SD ', 401.811, 168.833, 254.528], ['A', ' CE ', 400.985, 167.711, 253.373], ['A', ' H ', 397.286, 167.841, 257.598], ['A', ' HA ', 399.025, 170.241, 257.765], ['A', '1HB ', 400.381, 168.312, 256.993], ['A', '2HB ', 399.202, 167.998, 255.732], ['A', '1HG ', 399.774, 170.107, 254.618], ['A', '2HG ', 400.866, 170.522, 255.94], ['A', '1HE ', 401.739, 167.155, 252.815], ['A', '2HE ', 400.354, 167.013, 253.913], ['A', '3HE ', 400.374, 168.271, 252.68]]
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[['A', ' N ', 385.053, 211.001, 177.152], ['A', ' CA ', 385.713, 211.067, 178.449], ['A', ' C ', 387.093, 210.517, 178.24], ['A', ' O ', 387.97, 211.038, 178.926], ['A', ' CB ', 384.961, 210.33, 179.561], ['A', ' CG ', 383.704, 211.038, 180.046], ['A', ' ND1', 383.745, 212.132, 180.899], ['A', ' CD2', 382.4, 210.82, 179.789], ['A', ' CE1', 382.51, 212.537, 181.151], ['A', ' NE2', 381.68, 211.76, 180.497], ['A', ' H ', 385.359, 210.257, 176.542], ['A', ' HA ', 385.816, 212.105, 178.76], ['A', '1HB ', 384.662, 209.341, 179.204], ['A', '2HB ', 385.624, 210.186, 180.41], ['A', ' HD1', 384.542, 212.718, 181.034], ['A', ' HD2', 381.891, 210.08, 179.169], ['A', ' HE1', 382.327, 213.388, 181.806]]
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[['A', ' N ', 415.062, 166.967, 216.558], ['A', ' CA ', 416.273, 167.648, 216.094], ['A', ' C ', 416.719, 168.702, 217.099], ['A', ' O ', 417.903, 168.801, 217.427], ['A', ' CB ', 416.053, 168.35, 214.747], ['A', ' CG ', 415.914, 167.452, 213.555], ['A', ' CD ', 415.738, 168.27, 212.287], ['A', ' CE ', 415.697, 167.395, 211.075], ['A', ' NZ ', 414.547, 166.472, 211.111], ['A', ' H ', 414.175, 167.046, 216.05], ['A', ' HA ', 417.064, 166.913, 215.982], ['A', '1HB ', 415.146, 168.957, 214.808], ['A', '2HB ', 416.881, 169.031, 214.558], ['A', '1HG ', 416.797, 166.823, 213.471], ['A', '2HG ', 415.043, 166.812, 213.712], ['A', '1HD ', 414.802, 168.827, 212.349], ['A', '2HD ', 416.557, 168.975, 212.19], ['A', '1HE ', 415.619, 168.016, 210.186], ['A', '2HE ', 416.615, 166.813, 211.022], ['A', '1HZ ', 414.513, 165.869, 210.301], ['A', '2HZ ', 414.626, 165.883, 211.928], ['A', '3HZ ', 413.673, 166.994, 211.154]]
[['A', ' N ', 415.755, 169.444, 217.658], ['A', ' CA ', 416.033, 170.53, 218.595], ['A', ' C ', 416.778, 170.044, 219.818], ['A', ' O ', 417.65, 170.738, 220.351], ['A', ' CB ', 414.726, 171.178, 219.032], ['A', ' H ', 414.788, 169.309, 217.349], ['A', ' HA ', 416.653, 171.266, 218.084], ['A', '1HB ', 414.931, 172.005, 219.706], ['A', '2HB ', 414.195, 171.54, 218.152], ['A', '3HB ', 414.112, 170.441, 219.543]]
[['A', ' N ', 416.463, 168.835, 220.242], ['A', ' CA ', 417.059, 168.256, 221.414], ['A', ' C ', 418.013, 167.125, 221.067], ['A', ' O ', 418.39, 166.334, 221.937], ['A', ' CB ', 415.932, 167.765, 222.312], ['A', ' CG ', 414.96, 168.9, 222.649], ['A', ' CD1', 413.639, 168.871, 222.185], ['A', ' CD2', 415.373, 170.015, 223.365], ['A', ' CE1', 412.767, 169.911, 222.437], ['A', ' CE2', 414.496, 171.058, 223.617], ['A', ' CZ ', 413.197, 171.003, 223.154], ['A', ' H ', 415.698, 168.338, 219.773], ['A', ' HA ', 417.63, 169.023, 221.935], ['A', '1HB ', 415.383, 166.981, 221.789], ['A', '2HB ', 416.332, 167.348, 223.234], ['A', ' HD1', 413.294, 168.012, 221.615], ['A', ' HD2', 416.402, 170.073, 223.727], ['A', ' HE1', 411.739, 169.868, 222.064], ['A', ' HE2', 414.832, 171.93, 224.181], ['A', ' HZ ', 412.514, 171.829, 223.354]]
[['A', ' N ', 418.419, 167.021, 219.816], ['A', ' CA ', 419.292, 165.928, 219.433], ['A', ' C ', 420.574, 165.974, 220.234], ['A', ' O ', 421.636, 166.379, 219.708], ['A', ' CB ', 419.583, 166.004, 217.926], ['A', ' CG ', 420.369, 164.849, 217.252], ['A', ' CD1', 419.53, 163.555, 217.293], ['A', ' CD2', 420.65, 165.251, 215.783], ['A', ' H ', 418.119, 167.698, 219.11], ['A', ' HA ', 418.779, 164.997, 219.666], ['A', '1HB ', 418.63, 166.05, 217.425], ['A', '2HB ', 420.104, 166.943, 217.727], ['A', ' HG ', 421.315, 164.671, 217.774], ['A', '1HD1', 420.075, 162.753, 216.8], ['A', '2HD1', 419.325, 163.26, 218.32], ['A', '3HD1', 418.585, 163.731, 216.774], ['A', '1HD2', 421.197, 164.454, 215.281], ['A', '2HD2', 419.7, 165.42, 215.273], ['A', '3HD2', 421.245, 166.168, 215.755]]
Please check result here: /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_005_alphafold2_ptm_model_4_seed_000_s2/daq_score_w9.pdb
Please open it in pymol and visualize it by putting the following command to Pymol:
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spectrum b, red_white_blue, all, -1,1
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gcc -O3 -c chkcmdline.c
gcc -O3 -c mrc.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -O3 -c readpdb.c -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
gcc -o TrimMapAtom main.c chkcmdline.o mrc.o readpdb.o -lm -O3 -msse4.2 -msse -msse2 -msse3 -mmmx -ftree-vectorize -ftree-vectorizer-verbose=3 -ffast-math -march=native -funroll-loops -fopenmp
/net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_004_alphafold2_ptm_model_5_seed_000_s2 existed
Origin: (356.44003, 155.44, 159.46)
Previous voxel size: 1.0
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resizing finished!
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Finished processing model input!
0 batch processing time 0.714738
1 batch processing time 0.696898
2 batch processing time 0.699778
3 batch processing time 0.699383
4 batch processing time 0.695227
5 batch processing time 0.698359
6 batch processing time 0.696288
7 batch processing time 0.691248
8 batch processing time 0.692591
9 batch processing time 0.698021
Our predictions are saved in /net/kihara/scratch/webdklab/em-server/9d089ca034a9340fc99ca25a77b27bc2//chain_9/DAQ/rank_004_alphafold2_ptm_model_5_seed_000_s2/prediction.txt, please have a check!
total different chains: {'A'}
[['A', ' N ', 318.179, 181.674, 262.524], ['A', ' CA ', 319.236, 182.57, 263.016], ['A', ' C ', 320.329, 182.748, 261.973], ['A', ' O ', 320.985, 183.79, 261.861], ['A', ' CB ', 319.834, 182.007, 264.3], ['A', ' CG ', 318.9, 182.0, 265.522], ['A', ' SD ', 318.362, 183.654, 266.04], ['A', ' CE ', 319.876, 184.344, 266.74], ['A', ' H ', 317.196, 181.946, 262.633], ['A', ' HA ', 318.799, 183.545, 263.217], ['A', '1HB ', 320.13, 180.971, 264.122], ['A', '2HB ', 320.737, 182.55, 264.55], ['A', '1HG ', 318.011, 181.408, 265.288], ['A', '2HG ', 319.401, 181.519, 266.362], ['A', '1HE ', 319.688, 185.353, 267.116], ['A', '2HE ', 320.218, 183.71, 267.569], ['A', '3HE ', 320.65, 184.39, 265.976]]
[['A', ' N ', 320.497, 181.713, 261.175], ['A', ' CA ', 321.543, 181.654, 260.16], ['A', ' C ', 321.062, 182.384, 258.883], ['A', ' O ', 320.802, 181.78, 257.854], ['A', ' CB ', 321.828, 180.158, 259.942], ['A', ' CG ', 322.948, 179.801, 259.095], ['A', ' CD ', 323.205, 178.291, 259.028], ['A', ' OE1', 324.272, 177.874, 259.404], ['A', ' OE2', 322.342, 177.573, 258.602], ['A', ' H ', 319.873, 180.923, 261.312], ['A', ' HA ', 322.435, 182.155, 260.535], ['A', '1HB ', 322.002, 179.699, 260.915], ['A', '2HB ', 320.934, 179.691, 259.528], ['A', '1HG ', 322.702, 180.143, 258.112], ['A', '2HG ', 323.844, 180.317, 259.434]]
[['A', ' N ', 320.97, 183.727, 258.991], ['A', ' CA ', 320.393, 184.589, 257.938], ['A', ' C ', 321.367, 185.537, 257.202], ['A', ' O ', 320.944, 186.501, 256.562], ['A', ' CB ', 319.241, 185.415, 258.522], ['A', ' CG ', 317.984, 184.565, 258.935], ['A', ' OD1', 317.314, 183.938, 258.104], ['A', ' ND2', 317.675, 184.571, 260.209], ['A', ' H ', 321.222, 184.11, 259.912], ['A', ' HA ', 319.97, 183.933, 257.177], ['A', '1HB ', 319.6, 185.951, 259.402], ['A', '2HB ', 318.928, 186.158, 257.792], ['A', '1HD2', 316.877, 184.064, 260.531], ['A', '2HD2', 318.22, 185.106, 260.854]]
[['A', ' N ', 322.647, 185.256, 257.262], ['A', ' CA ', 323.69, 186.059, 256.613], ['A', ' C ', 323.915, 185.68, 255.166], ['A', ' O ', 324.694, 186.279, 254.428], ['A', ' CB ', 324.978, 185.85, 257.362], ['A', ' OG ', 325.37, 184.495, 257.276], ['A', ' H ', 322.929, 184.444, 257.796], ['A', ' HA ', 323.399, 187.112, 256.656], ['A', '1HB ', 325.76, 186.484, 256.935], ['A', '2HB ', 324.85, 186.136, 258.403], ['A', ' HG ', 326.216, 184.44, 257.733]]
[['A', ' N ', 323.249, 184.635, 254.78], ['A', ' CA ', 323.43, 183.969, 253.525], ['A', ' C ', 322.741, 184.64, 252.372], ['A', ' O ', 321.793, 184.133, 251.775], ['A', ' CB ', 323.012, 182.551, 253.811], ['A', ' CG ', 323.975, 182.031, 254.854], ['A', ' SD ', 323.715, 180.476, 255.449], ['A', ' CE ', 325.034, 180.541, 256.652], ['A', ' H ', 322.586, 184.257, 255.443], ['A', ' HA ', 324.499, 183.969, 253.307], ['A', '1HB ', 321.993, 182.529, 254.204], ['A', '2HB ', 323.056, 181.95, 252.902], ['A', '1HG ', 324.967, 182.053, 254.404], ['A', '2HG ', 324.004, 182.687, 255.712], ['A', '1HE ', 325.085, 179.59, 257.182], ['A', '2HE ', 325.989, 180.722, 256.156], ['A', '3HE ', 324.842, 181.347, 257.364]]
[['A', ' N ', 323.284, 185.782, 252.086], ['A', ' CA ', 322.889, 186.725, 251.087], ['A', ' C ', 324.166, 187.409, 250.579], ['A', ' O ', 325.129, 186.653, 250.515], ['A', ' CB ', 321.878, 187.706, 251.65], ['A', ' CG ', 320.587, 187.172, 252.055], ['A', ' SD ', 319.484, 188.448, 252.633], ['A', ' CE ', 318.967, 189.318, 251.162], ['A', ' H ', 324.062, 186.047, 252.697], ['A', ' HA ', 322.426, 186.191, 250.257], ['A', '1HB ', 322.284, 188.051, 252.557], ['A', '2HB ', 321.754, 188.534, 250.976], ['A', '1HG ', 320.12, 186.637, 251.232], ['A', '2HG ', 320.726, 186.465, 252.876], ['A', '1HE ', 318.275, 190.117, 251.438], ['A', '2HE ', 319.828, 189.757, 250.663], ['A', '3HE ', 318.466, 188.631, 250.48]]
[['A', ' N ', 323.941, 188.175, 249.533], ['A', ' CA ', 324.867, 189.296, 249.347], ['A', ' C ', 326.268, 188.967, 248.888], ['A', ' O ', 327.199, 189.634, 249.322], ['A', ' CB ', 325.148, 190.022, 250.672], ['A', ' CG ', 324.052, 190.427, 251.493], ['A', ' CD1', 324.03, 190.026, 252.788], ['A', ' CD2', 323.074, 191.215, 251.019], ['A', ' CE1', 323.041, 190.412, 253.608], ['A', ' CE2', 322.071, 191.603, 251.823], ['A', ' CZ ', 322.054, 191.195, 253.131], ['A', ' H ', 323.792, 187.655, 248.683], ['A', ' HA ', 324.428, 189.977, 248.627], ['A', '1HB ', 325.803, 189.408, 251.297], ['A', '2HB ', 325.718, 190.914, 250.471], ['A', ' HD1', 324.836, 189.392, 253.168], ['A', ' HD2', 323.09, 191.538, 249.979], ['A', ' HE1', 323.027, 190.081, 254.651], ['A', ' HE2', 321.271, 192.233, 251.444], ['A', ' HZ ', 321.244, 191.515, 253.79]]
[['A', ' N ', 326.485, 187.963, 248.069], ['A', ' CA ', 327.86, 187.849, 247.619], ['A', ' C ', 328.085, 189.049, 246.68], ['A', ' O ', 327.279, 189.28, 245.787], ['A', ' CB ', 328.158, 186.461, 246.935], ['A', ' CG1', 329.69, 186.352, 246.789], ['A', ' CG2', 327.378, 186.266, 245.557], ['A', ' CD1', 330.228, 184.983, 246.483], ['A', ' H ', 325.757, 187.355, 247.783], ['A', ' HA ', 328.529, 187.947, 248.472], ['A', ' HB ', 327.864, 185.683, 247.629], ['A', '1HG1', 329.977, 187.019, 245.99], ['A', '2HG1', 330.146, 186.687, 247.724], ['A', '1HG2', 327.609, 185.28, 245.12], ['A', '2HG2', 326.32, 186.336, 245.716], ['A', '3HG2', 327.683, 187.035, 244.83], ['A', '1HD1', 331.311, 185.053, 246.399], ['A', '2HD1', 329.962, 184.304, 247.296], ['A', '3HD1', 329.817, 184.613, 245.544]]
[['A', ' N ', 329.209, 189.767, 246.862], ['A', ' CA ', 329.562, 190.924, 246.057], ['A', ' C ', 328.65, 192.157, 246.273], ['A', ' O ', 327.861, 192.5, 245.38], ['A', ' CB ', 329.565, 190.536, 244.587], ['A', ' OG ', 330.289, 191.457, 243.807], ['A', ' H ', 329.801, 189.512, 247.628], ['A', ' HA ', 330.579, 191.222, 246.333], ['A', '1HB ', 330.001, 189.533, 244.485], ['A', '2HB ', 328.556, 190.484, 244.191], ['A', ' HG ', 330.247, 191.125, 242.908]]
[['A', ' N ', 328.705, 192.818, 247.458], ['A', ' CA ', 327.836, 194.013, 247.676], ['A', ' C ', 328.498, 195.335, 248.03], ['A', ' O ', 327.806, 196.32, 248.261], ['A', ' CB ', 326.739, 193.733, 248.684], ['A', ' CG ', 325.698, 192.729, 248.233], ['A', ' CD ', 324.833, 193.222, 247.134], ['A', ' NE ', 323.877, 192.26, 246.783], ['A', ' CZ ', 324.071, 191.279, 245.905], ['A', ' NH1', 325.215, 191.134, 245.281], ['A', ' NH2', 323.088, 190.441, 245.666], ['A', ' H ', 329.342, 192.509, 248.18], ['A', ' HA ', 327.342, 194.207, 246.734], ['A', '1HB ', 327.177, 193.335, 249.598], ['A', '2HB ', 326.212, 194.648, 248.946], ['A', '1HG ', 326.204, 191.817, 247.91], ['A', '2HG ', 325.052, 192.512, 249.058], ['A', '1HD ', 324.312, 194.119, 247.48], ['A', '2HD ', 325.399, 193.473, 246.242], ['A', ' HE ', 322.967, 192.327, 247.224], ['A', '1HH1', 326.025, 191.762, 245.44], ['A', '2HH1', 325.35, 190.373, 244.627], ['A', '1HH2', 322.202, 190.553, 246.142], ['A', '2HH2', 323.212, 189.687, 245.003]]
[['A', ' N ', 329.82, 195.383, 248.036], ['A', ' CA ', 330.546, 196.627, 248.275], ['A', ' C ', 331.287, 197.016, 247.01], ['A', ' O ', 332.121, 197.917, 246.997], ['A', ' CB ', 331.524, 196.452, 249.41], ['A', ' OG ', 332.454, 195.448, 249.116], ['A', ' H ', 330.373, 194.552, 247.896], ['A', ' HA ', 329.84, 197.417, 248.525], ['A', '1HB ', 332.041, 197.388, 249.582], ['A', '2HB ', 330.982, 196.2, 250.323], ['A', ' HG ', 333.108, 195.485, 249.825]]
[['A', ' N ', 330.998, 196.283, 245.946], ['A', ' CA ', 331.671, 196.399, 244.665], ['A', ' C ', 330.827, 197.017, 243.559], ['A', ' O ', 331.05, 196.744, 242.38], ['A', ' CB ', 332.166, 195.005, 244.247], ['A', ' CG ', 333.206, 194.289, 245.251], ['A', ' CD1', 333.495, 192.889, 244.74], ['A', ' CD2', 334.492, 195.091, 245.387], ['A', ' H ', 330.269, 195.594, 246.039], ['A', ' HA ', 332.528, 197.05, 244.798], ['A', '1HB ', 331.302, 194.348, 244.144], ['A', '2HB ', 332.65, 195.083, 243.271], ['A', ' HG ', 332.75, 194.191, 246.235], ['A', '1HD1', 334.177, 192.386, 245.427], ['A', '2HD1', 332.565, 192.33, 244.683], ['A', '3HD1', 333.947, 192.946, 243.754], ['A', '1HD2', 335.165, 194.581, 246.072], ['A', '2HD2', 334.968, 195.194, 244.414], ['A', '3HD2', 334.268, 196.079, 245.788]]
[['A', ' N ', 329.821, 197.796, 243.926], ['A', ' CA ', 328.977, 198.447, 242.925], ['A', ' C ', 329.502, 199.803, 242.478], ['A', ' O ', 329.587, 200.723, 243.284], ['A', ' CB ', 327.574, 198.638, 243.478], ['A', ' CG ', 326.583, 199.298, 242.534], ['A', ' CD ', 325.199, 199.358, 243.118], ['A', ' NE ', 324.599, 198.037, 243.216], ['A', ' CZ ', 323.972, 197.391, 242.202], ['A', ' NH1', 323.837, 197.956, 241.025], ['A', ' NH2', 323.491, 196.18, 242.393], ['A', ' H ', 329.666, 197.975, 244.905], ['A', ' HA ', 328.921, 197.795, 242.051], ['A', '1HB ', 327.169, 197.672, 243.767], ['A', '2HB ', 327.626, 199.252, 244.375], ['A', '1HG ', 326.897, 200.322, 242.331], ['A', '2HG ', 326.551, 198.74, 241.598], ['A', '1HD ', 325.259, 199.777, 244.123], ['A', '2HD ', 324.56, 199.993, 242.509], ['A', ' HE ', 324.671, 197.557, 244.106], ['A', '1HH1', 324.199, 198.882, 240.859], ['A', '2HH1', 323.368, 197.461, 240.277], ['A', '1HH2', 323.589, 195.735, 243.295], ['A', '2HH2', 323.024, 195.693, 241.641]]
[['A', ' N ', 329.813, 199.932, 241.175], ['A', ' CA ', 330.307, 201.199, 240.59], ['A', ' C ', 330.032, 201.236, 239.082], ['A', ' O ', 330.12, 200.209, 238.418], ['A', ' CB ', 331.841, 201.369, 240.727], ['A', ' CG ', 332.742, 200.677, 239.603], ['A', ' CD ', 332.733, 199.184, 239.705], ['A', ' NE ', 333.522, 198.518, 238.667], ['A', ' CZ ', 333.068, 198.164, 237.445], ['A', ' NH1', 331.826, 198.427, 237.078], ['A', ' NH2', 333.878, 197.532, 236.616], ['A', ' H ', 329.706, 199.117, 240.589], ['A', ' HA ', 329.811, 202.009, 241.112], ['A', '1HB ', 332.084, 202.428, 240.713], ['A', '2HB ', 332.16, 200.977, 241.692], ['A', '1HG ', 332.457, 200.985, 238.604], ['A', '2HG ', 333.773, 200.987, 239.767], ['A', '1HD ', 333.159, 198.91, 240.669], ['A', '2HD ', 331.734, 198.791, 239.661], ['A', ' HE ', 334.479, 198.279, 238.899], ['A', '1HH1', 331.182, 198.926, 237.716], ['A', '2HH1', 331.5, 198.149, 236.165], ['A', '1HH2', 334.828, 197.322, 236.899], ['A', '2HH2', 333.553, 197.255, 235.703]]
[['A', ' N ', 329.687, 202.394, 238.519], ['A', ' CA ', 329.581, 202.573, 237.091], ['A', ' C ', 330.978, 202.82, 236.529], ['A', ' O ', 331.799, 203.423, 237.202], ['A', ' CB ', 328.736, 203.841, 237.008], ['A', ' CG ', 329.093, 204.609, 238.266], ['A', ' CD ', 329.346, 203.552, 239.321], ['A', ' HA ', 329.099, 201.72, 236.624], ['A', '1HB ', 328.972, 204.391, 236.08], ['A', '2HB ', 327.668, 203.572, 236.954], ['A', '1HG ', 329.99, 205.231, 238.073], ['A', '2HG ', 328.284, 205.305, 238.53], ['A', '1HD ', 330.2, 203.873, 239.934], ['A', '2HD ', 328.429, 203.38, 239.906]]
[['A', ' N ', 331.193, 202.432, 235.273], ['A', ' CA ', 332.404, 202.844, 234.58], ['A', ' C ', 331.973, 203.45, 233.275], ['A', ' O ', 331.33, 202.784, 232.467], ['A', ' CB ', 333.372, 201.676, 234.368], ['A', ' CG1', 334.593, 202.128, 233.605], ['A', ' CG2', 333.786, 201.155, 235.719], ['A', ' H ', 330.496, 201.895, 234.78], ['A', ' HA ', 332.908, 203.608, 235.166], ['A', ' HB ', 332.882, 200.89, 233.794], ['A', '1HG1', 335.267, 201.285, 233.474], ['A', '2HG1', 334.304, 202.509, 232.622], ['A', '3HG1', 335.102, 202.916, 234.161], ['A', '1HG2', 334.476, 200.326, 235.594], ['A', '2HG2', 334.276, 201.951, 236.282], ['A', '3HG2', 332.922, 200.823, 236.256]]
[['A', ' N ', 332.315, 204.706, 233.062], ['A', ' CA ', 331.891, 205.392, 231.864], ['A', ' C ', 333.035, 206.08, 231.129], ['A', ' O ', 333.692, 206.942, 231.72], ['A', ' CB ', 330.922, 206.486, 232.285], ['A', ' OG1', 331.638, 207.39, 233.145], ['A', ' CG2', 329.732, 205.88, 233.075], ['A', ' H ', 332.851, 205.208, 233.751], ['A', ' HA ', 331.415, 204.679, 231.193], ['A', ' HB ', 330.561, 207.018, 231.404], ['A', ' HG1', 332.397, 207.77, 232.642], ['A', '1HG2', 329.061, 206.679, 233.381], ['A', '2HG2', 329.197, 205.177, 232.441], ['A', '3HG2', 330.086, 205.364, 233.961]]
[['A', ' N ', 333.253, 205.773, 229.832], ['A', ' CA ', 334.314, 206.444, 229.052], ['A', ' C ', 334.299, 206.146, 227.533], ['A', ' O ', 335.327, 205.719, 227.005], ['A', ' CB ', 335.689, 206.05, 229.595], ['A', ' H ', 332.689, 205.055, 229.399], ['A', ' HA ', 334.181, 207.518, 229.182], ['A', '1HB ', 336.46, 206.595, 229.044], ['A', '2HB ', 335.775, 206.297, 230.653], ['A', '3HB ', 335.839, 204.981, 229.466]]
[['A', ' N ', 333.18, 206.337, 226.821], ['A', ' CA ', 333.17, 206.016, 225.371], ['A', ' C ', 332.822, 207.201, 224.444], ['A', ' O ', 331.957, 208.014, 224.778], ['A', ' CB ', 332.154, 204.901, 225.094], ['A', ' CG ', 332.34, 203.556, 225.856], ['A', ' CD1', 331.156, 202.669, 225.532], ['A', ' CD2', 333.654, 202.875, 225.466], ['A', ' H ', 332.351, 206.71, 227.266], ['A', ' HA ', 334.16, 205.679, 225.091], ['A', '1HB ', 331.161, 205.279, 225.329], ['A', '2HB ', 332.187, 204.676, 224.031], ['A', ' HG ', 332.34, 203.736, 226.927], ['A', '1HD1', 331.247, 201.724, 226.064], ['A', '2HD1', 330.234, 203.168, 225.832], ['A', '3HD1', 331.131, 202.478, 224.459], ['A', '1HD2', 333.747, 201.931, 226.004], ['A', '2HD2', 333.661, 202.678, 224.393], ['A', '3HD2', 334.498, 203.512, 225.721]]
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