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logs1.txt
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MODELLER 9.19, 2017/07/19, r11078
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2017 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux PS 4.15.0-36-generic x86_64
Date and time of compilation : 2017/07/19 15:03:51
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2018/10/16 19:05:09
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL9v19}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL9v19}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183
openf___224_> Open ${MODINSTALL9v19}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL9v19}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242
openf___224_> Open ${MODINSTALL9v19}/modlib/radii14.lib
openf___224_> Open ${MODINSTALL9v19}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL9v19}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL9v19}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL9v19}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL9v19}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL9v19}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
# This file have all the modeller python file, Which will run one by one.
# [1] Build_profile.py
# [2] Compare.py
# [3] Align2d.py
# [4] Modelssingle.py
# [5] Evaluate_model.py
###################################################################################################
# Build_Profile.py
###################################################################################################
**** Name of "Selected_PDB" is = D3GDN9
**** File name is = D3GDN9.ali
openf___224_> Open pdb_95.pir
readlinef__W> File: pdb_95.pir, Line: 407
Modeller will only read the first 4096 characters of this line.
readlinef__W> File: pdb_95.pir, Line: 27190
Modeller will only read the first 4096 characters of this line.
readlinef__W> File: pdb_95.pir, Line: 27200
Modeller will only read the first 4096 characters of this line.
readlinef__W> File: pdb_95.pir, Line: 27210
Modeller will only read the first 4096 characters of this line.
readlinef__W> File: pdb_95.pir, Line: 27217
Modeller will only read the first 4096 characters of this line.
readlinef__W> File: pdb_95.pir, Line: 27223
No more warnings will be printed for truncated lines in this file.
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 494216 482.633 0.471
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3670718 3584.686 3.501
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3672560 3586.484 3.502
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3674010 3587.900 3.504
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3676910 3590.732 3.507
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 15663909 15296.786 14.938
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15669709 15302.450 14.944
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15681309 15313.778 14.955
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15704509 15336.435 14.977
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15750909 15381.747 15.021
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15843709 15472.372 15.110
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 21837209 21325.398 20.826
SEQ_DATABASE_FILE : pdb_95.pir
SEQ_DATABASE_FORMAT : PIR
CHAINS_LIST : ALL
CLEAN_SEQUENCES : T
MINMAX_DB_SEQ_LEN : 30 4000
Number of sequences : 59935
Number of residues : 15163123
Length of longest sequence: 3725
###################################################################################################
# Build_Profile.py > Sequence,read()
###################################################################################################
SEQ_DATABASE_FILE : pdb_95.bin
SEQ_DATABASE_FORMAT : BINARY
SEARCH_CHAINS_LIST : ALL
Number of sequences : 59935
Number of residues : 15163123
Length of longest sequence: 3725
###################################################################################################
# Build_Profile.py > Sequence,write()
###################################################################################################
SEQ_DATABASE_FILE : pdb_95.bin
SEQ_DATABASE_FORMAT : BINARY
CHAINS_LIST : ALL
CLEAN_SEQUENCES : T
MINMAX_DB_SEQ_LEN : 0 999999
Number of sequences : 59935
Number of residues : 15163123
Length of longest sequence: 3725
###################################################################################################
# Build_Profile.py > Sequence,read_Binary()
###################################################################################################
openf___224_> Open /home/ps/Documents/Coding/Modeller/OnWorking/alignments/D3GDN9.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 496136 484.508 0.473
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 497586 485.924 0.475
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 500486 488.756 0.477
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 506286 494.420 0.483
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 517886 505.748 0.494
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 520342 508.146 0.496
Read the alignment from file : /home/ps/Documents/Coding/Modeller/OnWorking/alignments/D3GDN9.ali
Total number of alignment positions: 615
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 D3GDN0_SP 615 1 D3GDN0_SPOL
###################################################################################################
# Build_Profile.py > Appending, writing files in .ali()
###################################################################################################
Dynamically allocated memory at amaxprofile [B,KiB,MiB]: 523127 510.866 0.499
###################################################################################################
# Build_Profile.py > Alignment_To_Profile(converstion)
###################################################################################################
openf___224_> Open ${LIB}/blosum62.sim.mat
rdrrwgh_268_> Number of residue types: 21
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 852365 832.388 0.813
profile_iteration_> processing sequence: 1 615 1 0.0200000 0.0200000 0.0200000 1
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 858675 838.550 0.819
profile_iteration_> processing sequence: 5995 615 1 7.5500002 0.0012594 0.0000048 794
profile_iteration_> processing sequence: 11989 615 1 14.4499998 0.0012053 0.0000047 830
profile_iteration_> processing sequence: 17983 615 1 21.6200008 0.0012022 0.0000047 832
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 859974 839.818 0.820
profile_iteration_> processing sequence: 23977 615 1 28.9899998 0.0012091 0.0000047 827
profile_iteration_> processing sequence: 29971 615 1 35.5800018 0.0011871 0.0000047 842
profile_iteration_> processing sequence: 35965 615 1 42.2599983 0.0011750 0.0000047 851
profile_iteration_> processing sequence: 41959 615 1 49.5600014 0.0011812 0.0000047 847
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 860799 840.624 0.821
profile_iteration_> processing sequence: 47953 615 1 57.8100014 0.0012056 0.0000048 829
Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 871807 851.374 0.831
profile_iteration_> processing sequence: 53947 615 1 65.6999969 0.0012179 0.0000048 821
AVERAGE RESIDUAL STANDARD ERROR: 29.30218
AVERAGE RESIDUAL STANDARD DEVIATION: 241.6994
profile_660_> Quality of the fit between observed/expected score distributions.
[Iteration, Chi2, nbins, KS-Stat, nscores ] = 1, 0.0172, 121, 0.0108, 59935
HISTOGRAM OF Z-SCORES:
Z: 1 -3.95000 0.00000 0.00000
Z: 1 -3.85000 0.00000 0.00000
Z: 1 -3.75000 0.00000 0.00000
Z: 1 -3.65000 0.00000 0.00000
Z: 1 -3.55000 0.00000 0.00000
Z: 1 -3.45000 0.00000 0.00000
Z: 1 -3.35000 0.00000 0.00000
Z: 1 -3.25000 0.00000 0.00000
Z: 1 -3.15000 0.00017 0.00000
Z: 1 -3.05000 0.00000 0.00000
Z: 1 -2.95000 0.00000 0.00000
Z: 1 -2.85000 0.00017 0.00000
Z: 1 -2.75000 0.00000 0.00000
Z: 1 -2.65000 0.00000 0.00000
Z: 1 -2.55000 0.00000 0.00001
Z: 1 -2.45000 0.00067 0.00004
Z: 1 -2.35000 0.00033 0.00016
Z: 1 -2.25000 0.00083 0.00055
Z: 1 -2.15000 0.00234 0.00163
Z: 1 -2.05000 0.00350 0.00416
Z: 1 -1.95000 0.01001 0.00933
Z: 1 -1.85000 0.01969 0.01872
Z: 1 -1.75000 0.04205 0.03400
Z: 1 -1.65000 0.06307 0.05658
Z: 1 -1.55000 0.07708 0.08721
Z: 1 -1.45000 0.13014 0.12565
Z: 1 -1.35000 0.15600 0.17059
Z: 1 -1.25000 0.23208 0.21981
Z: 1 -1.15000 0.25961 0.27052
Z: 1 -1.05000 0.33186 0.31973
Z: 1 -0.95000 0.35822 0.36469
Z: 1 -0.85000 0.40594 0.40316
Z: 1 -0.75000 0.40594 0.43360
Z: 1 -0.65000 0.47118 0.45519
Z: 1 -0.55000 0.45199 0.46779
Z: 1 -0.45000 0.46784 0.47182
Z: 1 -0.35000 0.45583 0.46811
Z: 1 -0.25000 0.42813 0.45775
Z: 1 -0.15000 0.42246 0.44196
Z: 1 -0.05000 0.42680 0.42194
Z: 1 0.05000 0.41495 0.39889
Z: 1 0.15000 0.38175 0.37383
Z: 1 0.25000 0.34838 0.34769
Z: 1 0.35000 0.32685 0.32121
Z: 1 0.45000 0.29699 0.29500
Z: 1 0.55000 0.27113 0.26953
Z: 1 0.65000 0.25644 0.24513
Z: 1 0.75000 0.22241 0.22205
Z: 1 0.85000 0.20155 0.20043
Z: 1 0.95000 0.17836 0.18036
Z: 1 1.05000 0.15717 0.16185
Z: 1 1.15000 0.14449 0.14489
Z: 1 1.25000 0.12447 0.12944
Z: 1 1.35000 0.11479 0.11542
Z: 1 1.45000 0.11012 0.10275
Z: 1 1.55000 0.08926 0.09133
Z: 1 1.65000 0.08743 0.08109
Z: 1 1.75000 0.07525 0.07191
Z: 1 1.85000 0.06424 0.06371
Z: 1 1.95000 0.05523 0.05639
Z: 1 2.05000 0.04972 0.04988
Z: 1 2.15000 0.04221 0.04409
Z: 1 2.25000 0.04405 0.03895
Z: 1 2.35000 0.03103 0.03439
Z: 1 2.45000 0.03370 0.03035
Z: 1 2.55000 0.02736 0.02678
Z: 1 2.65000 0.02002 0.02361
Z: 1 2.75000 0.02019 0.02082
Z: 1 2.85000 0.02419 0.01835
Z: 1 2.95000 0.01602 0.01617
Z: 1 3.05000 0.01351 0.01424
Z: 1 3.15000 0.01318 0.01255
Z: 1 3.25000 0.01068 0.01105
Z: 1 3.35000 0.01001 0.00973
Z: 1 3.45000 0.00851 0.00857
Z: 1 3.55000 0.00751 0.00754
Z: 1 3.65000 0.00751 0.00664
Z: 1 3.75000 0.00651 0.00584
Z: 1 3.85000 0.00501 0.00514
Z: 1 3.95000 0.00467 0.00453
Z: 1 4.05000 0.00484 0.00398
Z: 1 4.15000 0.00434 0.00350
Z: 1 4.25000 0.00534 0.00308
Z: 1 4.35000 0.00267 0.00271
Z: 1 4.45000 0.00317 0.00239
Z: 1 4.55000 0.00300 0.00210
Z: 1 4.65000 0.00167 0.00185
Z: 1 4.75000 0.00184 0.00163
Z: 1 4.85000 0.00150 0.00143
Z: 1 4.95000 0.00234 0.00126
Z: 1 5.05000 0.00184 0.00111
Z: 1 5.15000 0.00234 0.00097
Z: 1 5.25000 0.00100 0.00086
Z: 1 5.35000 0.00117 0.00075
Z: 1 5.45000 0.00100 0.00066
Z: 1 5.55000 0.00100 0.00058
Z: 1 5.65000 0.00150 0.00051
Z: 1 5.75000 0.00050 0.00045
Z: 1 5.85000 0.00050 0.00040
Z: 1 5.95000 0.00100 0.00035
Z: 1 6.05000 0.00083 0.00031
Z: 1 6.15000 0.00000 0.00027
Z: 1 6.25000 0.00017 0.00024
Z: 1 6.35000 0.00050 0.00021
Z: 1 6.45000 0.00033 0.00018
Z: 1 6.55000 0.00033 0.00016
Z: 1 6.65000 0.00050 0.00014
Z: 1 6.75000 0.00067 0.00013
Z: 1 6.85000 0.00033 0.00011
Z: 1 6.95000 0.00033 0.00010
Z: 1 7.05000 0.00050 0.00009
Z: 1 7.15000 0.00050 0.00007
Z: 1 7.25000 0.00017 0.00007
Z: 1 7.35000 0.00000 0.00006
Z: 1 7.45000 0.00000 0.00005
Z: 1 7.55000 0.00017 0.00004
Z: 1 7.65000 0.00000 0.00004
Z: 1 7.75000 0.00017 0.00003
Z: 1 7.85000 0.00017 0.00003
Z: 1 7.95000 0.00017 0.00003
Z: 1 8.05000 0.00000 0.00002
HITS FOUND IN ITERATION: 1
Dynamically allocated memory at amaxprofile [B,KiB,MiB]: 1380807 1348.444 1.317
> 5a2gA 1 243 12700 501 615 38.19 0.0 2 192 47 260 30 228
> 5a7gA 1 572 29350 529 615 33.59 0.0 3 503 20 574 3 529
> 3ainA 1 1214 5150 283 615 37.00 0.55E-03 4 97 124 233 33 132
> 1aknA 1 1316 23800 547 615 30.20 0.0 5 479 44 579 27 536
> 5ao9A 1 1639 4600 280 615 26.58 0.10E-01 6 141 116 263 16 173
> 6aryA 1 1874 23300 537 615 31.83 0.0 7 496 19 576 2 532
> 3b3qA 1 2728 27450 536 615 32.64 0.0 8 468 44 547 26 509
> 2bceA 1 3410 23500 532 615 30.41 0.0 9 469 47 572 30 519
> 4bdtA 1 3493 25450 563 615 31.70 0.0 10 502 30 576 7 536
> 3be8A 1 3549 30000 543 615 33.53 0.0 11 493 44 573 35 541
> 3be8B 1 3550 29650 534 615 33.93 0.0 12 490 44 573 29 532
> 4be9A 1 3570 13450 538 615 28.36 0.0 13 439 44 535 21 496
> 3bixA 1 3777 27000 555 615 32.61 0.0 14 449 44 525 26 485
> 3bl8A 1 3981 29500 556 615 32.83 0.0 15 494 44 573 27 553
> 3bl8C 1 3982 29650 545 615 33.14 0.0 16 489 44 573 26 541
> 1c7jA 1 5569 22300 485 615 37.19 0.0 17 426 49 548 25 465
> 2c7bA 1 5577 5450 295 615 35.48 0.12E-03 18 91 132 233 48 140
> 5ch5A 1 6379 18150 566 615 30.09 0.0 19 440 46 530 53 514
> 1crlA 1 7116 16000 534 615 30.79 0.0 20 432 46 537 22 492
> 5dtiA 1 10052 24100 539 615 29.81 0.0 21 515 19 576 8 537
> 5dtiB 1 10053 24500 529 615 29.92 0.0 22 515 19 576 2 529
> 1dx4A 1 10238 20000 537 615 29.60 0.0 23 469 27 575 8 534
> 6emiA 1 12276 27950 527 615 32.37 0.0 24 507 29 575 9 527
> 1f6wA 1 13839 24150 533 615 30.58 0.0 25 467 47 572 30 526
> 2fj0A 1 14904 17600 530 615 28.74 0.0 26 473 29 548 10 503
> 5fv4A 1 15780 31750 530 615 34.29 0.0 27 494 28 574 9 530
> 6g1uA 1 16180 24200 532 615 31.83 0.0 28 481 41 576 21 529
> 1gz7A 1 18405 16450 534 615 31.70 0.0 29 429 47 537 23 492
> 5hq3A 1 20405 26600 529 615 33.00 0.0 30 487 44 576 25 527
> 1jmyA 1 24860 23350 515 615 31.69 0.0 31 443 47 549 30 496
> 1k4yA 1 26135 27150 501 615 31.39 0.0 32 473 20 574 1 497
> 3k9bA 1 26538 27350 485 615 34.10 0.0 33 467 30 570 5 485
> 3k9bB 1 26539 27900 499 615 34.95 0.0 34 483 30 574 5 499
> 3k9bC 1 26540 27050 453 615 36.30 0.0 35 446 30 569 5 453
> 5lk6A 1 29958 5250 302 615 28.93 0.35E-03 36 184 124 322 53 249
> 1llfA 1 29967 16400 534 615 33.44 0.0 37 294 46 357 22 341
> 1lzlA 1 31042 5100 317 615 30.85 0.82E-03 38 92 133 233 68 161
> 4m0eA 1 31124 26350 532 615 32.12 0.0 39 501 30 576 8 530
> 2ogsA 1 37178 18750 478 615 33.48 0.0 40 431 44 557 19 469
> 2ogtA 1 37179 19100 463 615 33.72 0.0 41 420 44 557 19 454
> 1p0iA 1 38470 27500 523 615 33.53 0.0 42 484 29 575 8 523
> 1qe3A 1 41307 21450 467 615 36.24 0.0 43 413 49 548 25 449
> 3qh4A 1 41505 4750 314 615 32.26 0.52E-02 44 122 144 287 83 206
> 4qwwA 1 42378 27600 529 615 32.67 0.0 45 480 44 576 25 526
> 1thgA 1 46304 16800 543 615 33.53 0.0 46 298 43 358 19 352
> 5thmA 1 46337 14250 488 615 31.59 0.0 47 409 46 518 23 443
> 1ukcA 1 48578 14900 517 615 31.03 0.0 48 439 27 537 3 479
> 3vkfA 1 50738 27100 560 615 30.65 0.0 49 475 44 547 26 534
> 5w1uA 1 51679 13150 536 615 34.36 0.0 50 221 29 282 9 235
> 1w76A 1 52002 24750 522 615 32.46 0.0 51 471 41 576 21 519
> 3wj1A 1 52950 5350 304 615 27.41 0.21E-03 52 184 124 322 53 249
> 4wy5A 1 54061 5550 320 615 30.77 0.76E-04 53 115 111 234 45 161
> 4wy8A 1 54062 4850 325 615 25.31 0.32E-02 54 158 78 249 19 180
> 5xeqA 1 55138 28900 525 615 34.14 0.0 55 481 44 573 25 522
> 4zrsA 1 59481 6450 291 615 34.53 0.57E-06 56 132 112 260 38 176
> 3zwqA 1 59731 4650 313 615 26.80 0.88E-02 57 176 132 322 67 260
profile_iteration__> Weight Matrix [sec]: 0.020000
profile_iteration__> Score Collection [sec]: 73.260002
profile_iteration__> Score Collection/Seq [sec]: 0.001222
profile_iteration__> DP Steps per sec [ali/sec]: 818.784180
profile_iteration__> Statistics [sec]: 0.060000
profile_iteration__> Add to profile [sec]: 0.300000
profile_iteration__> Overall performance [/seq]: 0.001229
profile_iteration__> Overall performance [seq/sec]: 813.450073
###################################################################################################
# Build_Profile.py > Profile.Build()
###################################################################################################
openf___224_> Open /home/ps/Documents/Coding/Modeller/OnWorking/GST/PRF/D3GDN9_build_profile.prf
###################################################################################################
# Build_Profile.py > Writing, Profile in .prf
###################################################################################################
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1370330 1338.213 1.307
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1372786 1340.611 1.309
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1373550 1341.357 1.310
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1375558 1343.318 1.312
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1375942 1343.693 1.312
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1377854 1345.561 1.314
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1378414 1346.107 1.315
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1380394 1348.041 1.316
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1382262 1349.865 1.318
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1384134 1351.693 1.320
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1386138 1353.650 1.322
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1388106 1355.572 1.324
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1390062 1357.482 1.326
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1391814 1359.193 1.327
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1393606 1360.943 1.329
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1395578 1362.869 1.331
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1397530 1364.775 1.333
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1399230 1366.436 1.334
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1399590 1366.787 1.335
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1401346 1368.502 1.336
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1403070 1370.186 1.338
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1405126 1372.193 1.340
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1407182 1374.201 1.342
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1409054 1376.029 1.344
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1411078 1378.006 1.346
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1412942 1379.826 1.347
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1414830 1381.670 1.349
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1416802 1383.596 1.351
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1418722 1385.471 1.353
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1420434 1387.143 1.355
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1422378 1389.041 1.356
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1424146 1390.768 1.358
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1426034 1392.611 1.360
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1427898 1394.432 1.362
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1429826 1396.314 1.364
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1431606 1398.053 1.365
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1432338 1398.768 1.366
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1433510 1399.912 1.367
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1433874 1400.268 1.367
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1435874 1402.221 1.369
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1437594 1403.900 1.371
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1439270 1405.537 1.373
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1441202 1407.424 1.374
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1442850 1409.033 1.376
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1443334 1409.506 1.376
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1445250 1411.377 1.378
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1446438 1412.537 1.379
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1448070 1414.131 1.381
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1449822 1415.842 1.383
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1451718 1417.693 1.384
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1452598 1418.553 1.385
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1454478 1420.389 1.387
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1455210 1421.104 1.388
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1455666 1421.549 1.388
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1456294 1422.162 1.389
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1458214 1424.037 1.391
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1458738 1424.549 1.391
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1459438 1425.232 1.392
###################################################################################################
# Build_Profile.py > Profile To Alignment
###################################################################################################
openf___224_> Open /home/ps/Documents/Coding/Modeller/OnWorking/GST/ALI/D3GDN9_build_profile.ali
###################################################################################################
# Build_Profile.py > Writing ALignment from Profile
###################################################################################################
###################################################################################################
# Compare.py
###################################################################################################
This is the pdb_var: 5a2gA
This is the pdb_var: 5a7gA
This is the pdb_var: 3ainA
This is the pdb_var: 1aknA
This is the pdb_var: 5ao9A
This is the pdb_var: 6aryA
This is the pdb_var: 3b3qA
This is the pdb_var: 2bceA
This is the pdb_var: 4bdtA
This is the pdb_var: 3be8A
This is the pdb_var: 3be8B
This is the pdb_var: 4be9A
This is the pdb_var: 3bixA
This is the pdb_var: 3bl8A
This is the pdb_var: 3bl8C
This is the pdb_var: 1c7jA
This is the pdb_var: 2c7bA
This is the pdb_var: 5ch5A
This is the pdb_var: 1crlA
This is the pdb_var: 5dtiA
This is the pdb_var: 5dtiB
This is the pdb_var: 1dx4A
This is the pdb_var: 6emiA
This is the pdb_var: 1f6wA
This is the pdb_var: 2fj0A
This is the pdb_var: 5fv4A
This is the pdb_var: 6g1uA
This is the pdb_var: 1gz7A
This is the pdb_var: 5hq3A
This is the pdb_var: 1jmyA
This is the pdb_var: 1k4yA
This is the pdb_var: 3k9bA
This is the pdb_var: 3k9bB
This is the pdb_var: 3k9bC
This is the pdb_var: 5lk6A
This is the pdb_var: 1llfA
This is the pdb_var: 1lzlA
This is the pdb_var: 4m0eA
This is the pdb_var: 2ogsA
This is the pdb_var: 2ogtA
This is the pdb_var: 1p0iA
This is the pdb_var: 1qe3A
This is the pdb_var: 3qh4A
This is the pdb_var: 4qwwA
This is the pdb_var: 1thgA
This is the pdb_var: 5thmA
This is the pdb_var: 1ukcA
This is the pdb_var: 3vkfA
This is the pdb_var: 5w1uA
This is the pdb_var: 1w76A
This is the pdb_var: 3wj1A
This is the pdb_var: 4wy5A
This is the pdb_var: 4wy8A
This is the pdb_var: 5xeqA
This is the pdb_var: 4zrsA
This is the pdb_var: 3zwqA
This is the Profile File:
[[0.0, 38.0, 192.0, '5a2gA'], [0.0, 34.0, 503.0, '5a7gA'], [0.00055, 37.0, 97.0, '3ainA'], [0.0, 30.0, 479.0, '1aknA'], [0.01, 27.0, 141.0, '5ao9A'], [0.0, 32.0, 496.0, '6aryA'], [0.0, 33.0, 468.0, '3b3qA'], [0.0, 30.0, 469.0, '2bceA'], [0.0, 32.0, 502.0, '4bdtA'], [0.0, 34.0, 493.0, '3be8A'], [0.0, 34.0, 490.0, '3be8B'], [0.0, 28.0, 439.0, '4be9A'], [0.0, 33.0, 449.0, '3bixA'], [0.0, 33.0, 494.0, '3bl8A'], [0.0, 33.0, 489.0, '3bl8C'], [0.0, 37.0, 426.0, '1c7jA'], [0.00012, 35.0, 91.0, '2c7bA'], [0.0, 30.0, 440.0, '5ch5A'], [0.0, 31.0, 432.0, '1crlA'], [0.0, 30.0, 515.0, '5dtiA'], [0.0, 30.0, 515.0, '5dtiB'], [0.0, 30.0, 469.0, '1dx4A'], [0.0, 32.0, 507.0, '6emiA'], [0.0, 31.0, 467.0, '1f6wA'], [0.0, 29.0, 473.0, '2fj0A'], [0.0, 34.0, 494.0, '5fv4A'], [0.0, 32.0, 481.0, '6g1uA'], [0.0, 32.0, 429.0, '1gz7A'], [0.0, 33.0, 487.0, '5hq3A'], [0.0, 32.0, 443.0, '1jmyA'], [0.0, 31.0, 473.0, '1k4yA'], [0.0, 34.0, 467.0, '3k9bA'], [0.0, 35.0, 483.0, '3k9bB'], [0.0, 36.0, 446.0, '3k9bC'], [0.00035, 29.0, 184.0, '5lk6A'], [0.0, 33.0, 294.0, '1llfA'], [0.00082, 31.0, 92.0, '1lzlA'], [0.0, 32.0, 501.0, '4m0eA'], [0.0, 33.0, 431.0, '2ogsA'], [0.0, 34.0, 420.0, '2ogtA'], [0.0, 34.0, 484.0, '1p0iA'], [0.0, 36.0, 413.0, '1qe3A'], [0.0052, 32.0, 122.0, '3qh4A'], [0.0, 33.0, 480.0, '4qwwA'], [0.0, 34.0, 298.0, '1thgA'], [0.0, 32.0, 409.0, '5thmA'], [0.0, 31.0, 439.0, '1ukcA'], [0.0, 31.0, 475.0, '3vkfA'], [0.0, 34.0, 221.0, '5w1uA'], [0.0, 32.0, 471.0, '1w76A'], [0.00021, 27.0, 184.0, '3wj1A'], [7.6e-05, 31.0, 115.0, '4wy5A'], [0.0032, 25.0, 158.0, '4wy8A'], [0.0, 34.0, 481.0, '5xeqA'], [5.7e-07, 35.0, 132.0, '4zrsA'], [0.0088, 27.0, 176.0, '3zwqA']]
**** MaxE Name = 5a2gA
**** PDB Name = 5a2gA
**** PDb, Chains are: 5a2g A
openf___224_> Open /home/ps/Documents/Coding/Modeller/OnWorking/GST/PDB/5a2g.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1017473 993.626 0.970
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1017549 993.700 0.970
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1017720 993.867 0.971
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1018570 994.697 0.971
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1019828 995.926 0.973
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021732 997.785 0.974
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1021772 997.824 0.974
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1021862 997.912 0.975
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1024718 1000.701 0.977
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1024778 1000.760 0.977
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1024913 1000.892 0.977
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1029197 1005.075 0.982
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1035623 1011.351 0.988
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1035711 1011.437 0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1035909 1011.630 0.988
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1036041 1011.759 0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1036338 1012.049 0.988
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1045960 1021.445 0.998
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1046160 1021.641 0.998
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1046610 1022.080 0.998
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1061060 1036.191 1.012
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1061360 1036.484 1.012
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1062035 1037.144 1.013
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1083693 1058.294 1.033
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1084141 1058.731 1.034
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1085149 1059.716 1.035
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1117653 1091.458 1.066
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1118325 1092.114 1.067
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1119837 1093.591 1.068
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1168593 1141.204 1.114
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1516433 1480.892 1.446
read_mo_297_> Segments, residues, atoms: 1 501 3940
read_mo_298_> Segment: 1 2 A 502 A 3940
**** Model is Made
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1530933 1495.052 1.460
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1821718 1779.021 1.737
openf___224_> Open $(LIB)/as1.sim.mat
rdrrwgh_268_> Number of residue types: 20
Multiple dynamic programming alignment (MALIGN):
Residue-residue metric : $(LIB)/as1.sim.mat
ALIGN_BLOCK : 1
Gap introduction penalty: -900.0000
Gap extension penalty : -50.0000
Length of alignment : 501
malign3_327W> Only one structure; nothing done.
compare_343_> >> BEGINNING OF COMMAND
COMPARISON OF SEVERAL 3D STRUCTURES:
# ALGNMT CODE ATOM FILE
1 5a2gA
Variability at a given position is calculated as:
VAR = 1/Nij * sum_ij (feat_i - feat_j)
sum runs over all pairs of proteins with residues present.
>> Least-squares superposition (FIT) : T
Atom types for superposition/RMS (FIT_ATOMS): CA
Atom type for position average/variability (VARATOM): CA
Position comparison (FIT_ATOMS):
Cutoff for RMS calculation: 3.5000
Upper = RMS, Lower = numb equiv positions
5a2gA
5a2gA 0.000
Distance comparison (FIT_ATOMS):
Cutoff for rms calculation: 3.5000
Upper = Distance RMS, Lower = numb equiv distances
5a2gA
5a2gA 0.000
>> Sequence comparison:
Diag=numb res, Upper=numb equiv res, Lower = % seq ID
5a2gA
5a2gA 4
>> Dihedral angle comparison: Alph
Cutoff for rms comparison: 60.0000
Upper = RMS Alph, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: Phi
Cutoff for rms comparison: 60.0000
Upper = RMS Phi , Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: Psi
Cutoff for rms comparison: 15.0000
Upper = RMS Psi , Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: Omeg
Cutoff for rms comparison: 60.0000
Upper = RMS Omeg, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: chi1
Cutoff for rms comparison: 60.0000
Upper = RMS chi1, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: chi2
Cutoff for rms comparison: 60.0000
Upper = RMS chi2, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: chi3
Cutoff for rms comparison: 60.0000
Upper = RMS chi3, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: chi4
Cutoff for rms comparison: 60.0000
Upper = RMS chi4, Lower = numb of equiv angles
5a2gA
5a2gA 0.000
>> Dihedral angle comparison: chi5
Cutoff for rms comparison: 60.0000
Upper = RMS chi5, Lower = numb of equiv angles
5a2gA
5a2gA 0.000