MODELLER 9v4, 2008/05/09, r6267 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2008 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, 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 suse 2.6.22.17-0.1-default i686 Date and time of compilation : 2008/05/09 13:05:53 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2008/07/31 09:52:39 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v4}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v4}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234070 3158.271 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234598 3158.787 3.085 openf___224_> Open ${MODINSTALL9v4}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283198 3206.248 3.131 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 ${MODINSTALL9v4}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292174 3215.014 3.140 openf___224_> Open ${MODINSTALL9v4}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v4}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v4}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v4}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v4}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v4}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v4}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open pdb95.fsa Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3584463 3500.452 3.418 openf___224_> Open pdb95.fsa openf___224_> Open pdb95.fsa Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3586281 3502.228 3.420 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3587731 3503.644 3.422 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3590631 3506.476 3.424 Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 4692230 4582.256 4.475 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4698030 4587.920 4.480 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4709630 4599.248 4.491 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4732830 4621.904 4.514 Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 5283630 5159.795 5.039 SEQ_DATABASE_FILE : pdb95.fsa SEQ_DATABASE_FORMAT : FASTA CHAINS_LIST : ALL CLEAN_SEQUENCES : T MINMAX_DB_SEQ_LEN : 1 40000 Number of sequences : 5508 Number of residues : 1268520 Length of longest sequence: 1287 SEQ_DATABASE_FILE : pdb95.bin SEQ_DATABASE_FORMAT : BINARY SEARCH_CHAINS_LIST : ALL Number of sequences : 5508 Number of residues : 1268520 Length of longest sequence: 1287 SEQ_DATABASE_FILE : pdb95.bin SEQ_DATABASE_FORMAT : BINARY CHAINS_LIST : ALL CLEAN_SEQUENCES : T MINMAX_DB_SEQ_LEN : 0 999999 Number of sequences : 5508 Number of residues : 1268520 Length of longest sequence: 1287 openf___224_> Open link2_vWF.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 5238836 5116.051 4.996 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 5238952 5116.164 4.996 Read the alignment from file : link2_vWF.ali Total number of alignment positions: 30 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 link1_vWF 30 1 vWF Dynamically allocated memory at amaxprofile [B,KiB,MiB]: 5239373 5116.575 4.997 openf___224_> Open ${LIB}/blosum62.sim.mat rdrrwgh_268_> Number of residue types: 21 profile_iteration_> processing sequence: 1 30 1 0.0000000 0.0000000 0.0000000 1 profile_iteration_> processing sequence: 552 30 1 0.0800000 0.0001449 0.0000006 552 profile_iteration_> processing sequence: 1103 30 1 0.1600000 0.0001451 0.0000006 1103 profile_iteration_> processing sequence: 1654 30 1 0.2400000 0.0001451 0.0000006 1654 profile_iteration_> processing sequence: 2205 30 1 0.3200000 0.0001451 0.0000006 2205 profile_iteration_> processing sequence: 2756 30 1 0.4000000 0.0001451 0.0000006 2756 profile_iteration_> processing sequence: 3307 30 1 0.4800000 0.0001451 0.0000006 3307 profile_iteration_> processing sequence: 3858 30 1 0.5600000 0.0001452 0.0000006 3858 profile_iteration_> processing sequence: 4409 30 1 0.6300000 0.0001429 0.0000006 4409 profile_iteration_> processing sequence: 4960 30 1 0.7200000 0.0001452 0.0000006 4960 AVERAGE RESIDUAL STANDARD ERROR: 35.02277 AVERAGE RESIDUAL STANDARD DEVIATION: 190.4418 profile_660_> Quality of the fit between observed/expected score distributions. [Iteration, Chi2, nbins, KS-Stat, nscores ] = 1, 0.1692, 121, 0.0218, 5508 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 0.00000 0.00000 Z: 1 -3.05000 0.00000 0.00000 Z: 1 -2.95000 0.00000 0.00000 Z: 1 -2.85000 0.00000 0.00000 Z: 1 -2.75000 0.00000 0.00000 Z: 1 -2.65000 0.00000 0.00000 Z: 1 -2.55000 0.00182 0.00001 Z: 1 -2.45000 0.00000 0.00004 Z: 1 -2.35000 0.00000 0.00016 Z: 1 -2.25000 0.00545 0.00055 Z: 1 -2.15000 0.00182 0.00163 Z: 1 -2.05000 0.00726 0.00416 Z: 1 -1.95000 0.01816 0.00933 Z: 1 -1.85000 0.03813 0.01872 Z: 1 -1.75000 0.04720 0.03400 Z: 1 -1.65000 0.06718 0.05658 Z: 1 -1.55000 0.11438 0.08721 Z: 1 -1.45000 0.13798 0.12565 Z: 1 -1.35000 0.18337 0.17059 Z: 1 -1.25000 0.25962 0.21981 Z: 1 -1.15000 0.24147 0.27052 Z: 1 -1.05000 0.30683 0.31973 Z: 1 -0.95000 0.36129 0.36469 Z: 1 -0.85000 0.36311 0.40316 Z: 1 -0.75000 0.41757 0.43360 Z: 1 -0.65000 0.38671 0.45519 Z: 1 -0.55000 0.49201 0.46779 Z: 1 -0.45000 0.38853 0.47182 Z: 1 -0.35000 0.42484 0.46811 Z: 1 -0.25000 0.52288 0.45775 Z: 1 -0.15000 0.39942 0.44196 Z: 1 -0.05000 0.38853 0.42194 Z: 1 0.05000 0.37037 0.39889 Z: 1 0.15000 0.35403 0.37383 Z: 1 0.25000 0.34495 0.34769 Z: 1 0.35000 0.28686 0.32121 Z: 1 0.45000 0.31590 0.29500 Z: 1 0.55000 0.30864 0.26953 Z: 1 0.65000 0.23784 0.24513 Z: 1 0.75000 0.23784 0.22205 Z: 1 0.85000 0.18337 0.20043 Z: 1 0.95000 0.21060 0.18036 Z: 1 1.05000 0.19971 0.16185 Z: 1 1.15000 0.11438 0.14489 Z: 1 1.25000 0.13253 0.12944 Z: 1 1.35000 0.23602 0.11542 Z: 1 1.45000 0.10167 0.10275 Z: 1 1.55000 0.07625 0.09133 Z: 1 1.65000 0.08533 0.08109 Z: 1 1.75000 0.07262 0.07191 Z: 1 1.85000 0.08715 0.06371 Z: 1 1.95000 0.05084 0.05639 Z: 1 2.05000 0.07807 0.04988 Z: 1 2.15000 0.04539 0.04409 Z: 1 2.25000 0.03994 0.03895 Z: 1 2.35000 0.03994 0.03439 Z: 1 2.45000 0.03813 0.03035 Z: 1 2.55000 0.01816 0.02678 Z: 1 2.65000 0.01089 0.02361 Z: 1 2.75000 0.01634 0.02082 Z: 1 2.85000 0.02542 0.01835 Z: 1 2.95000 0.01997 0.01617 Z: 1 3.05000 0.02360 0.01424 Z: 1 3.15000 0.00908 0.01255 Z: 1 3.25000 0.00363 0.01105 Z: 1 3.35000 0.00726 0.00973 Z: 1 3.45000 0.00726 0.00857 Z: 1 3.55000 0.00363 0.00754 Z: 1 3.65000 0.00182 0.00664 Z: 1 3.75000 0.00182 0.00584 Z: 1 3.85000 0.00363 0.00514 Z: 1 3.95000 0.00545 0.00453 Z: 1 4.05000 0.00545 0.00398 Z: 1 4.15000 0.00363 0.00350 Z: 1 4.25000 0.00000 0.00308 Z: 1 4.35000 0.00000 0.00271 Z: 1 4.45000 0.00182 0.00239 Z: 1 4.55000 0.00000 0.00210 Z: 1 4.65000 0.00182 0.00185 Z: 1 4.75000 0.00000 0.00163 Z: 1 4.85000 0.00182 0.00143 Z: 1 4.95000 0.00182 0.00126 Z: 1 5.05000 0.00000 0.00111 Z: 1 5.15000 0.00000 0.00097 Z: 1 5.25000 0.00000 0.00086 Z: 1 5.35000 0.00182 0.00075 Z: 1 5.45000 0.00000 0.00066 Z: 1 5.55000 0.00000 0.00058 Z: 1 5.65000 0.00000 0.00051 Z: 1 5.75000 0.00000 0.00045 Z: 1 5.85000 0.00000 0.00040 Z: 1 5.95000 0.00000 0.00035 Z: 1 6.05000 0.00000 0.00031 Z: 1 6.15000 0.00000 0.00027 Z: 1 6.25000 0.00000 0.00024 Z: 1 6.35000 0.00000 0.00021 Z: 1 6.45000 0.00000 0.00018 Z: 1 6.55000 0.00000 0.00016 Z: 1 6.65000 0.00000 0.00014 Z: 1 6.75000 0.00000 0.00013 Z: 1 6.85000 0.00000 0.00011 Z: 1 6.95000 0.00000 0.00010 Z: 1 7.05000 0.00000 0.00009 Z: 1 7.15000 0.00000 0.00007 Z: 1 7.25000 0.00000 0.00007 Z: 1 7.35000 0.00000 0.00006 Z: 1 7.45000 0.00000 0.00005 Z: 1 7.55000 0.00000 0.00004 Z: 1 7.65000 0.00000 0.00004 Z: 1 7.75000 0.00000 0.00003 Z: 1 7.85000 0.00000 0.00003 Z: 1 7.95000 0.00000 0.00003 Z: 1 8.05000 0.00000 0.00002 HITS FOUND IN ITERATION: 1 profile_iteration__> Weight Matrix [sec]: 0.000000 profile_iteration__> Score Collection [sec]: 0.800000 profile_iteration__> Score Collection/Seq [sec]: 0.000145 profile_iteration__> DP Steps per sec [ali/sec]: 6885.000000 profile_iteration__> Statistics [sec]: 0.000000 profile_iteration__> Add to profile [sec]: 0.000000 profile_iteration__> Overall performance [/seq]: 0.000147 profile_iteration__> Overall performance [seq/sec]: 6800.000000 openf___224_> Open buildprofile.prf Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 5240767 5117.937 4.998 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 5240883 5118.050 4.998 openf___224_> Open buildprofile.ali Dynamically allocated memory at finish [B,KiB,MiB]: 5238793 5116.009 4.996 Starting time : 2008/07/31 09:52:39 Closing time : 2008/07/31 09:52:41 Total CPU time [seconds] : 1.74