MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 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 sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:41:50 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 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 ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open $(LIB)/top_allh.lib read_to_681_> topology.submodel read from topology file: 1 openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 465650 454.736 0.444 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 467250 456.299 0.446 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 471230 460.186 0.449 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 473230 462.139 0.451 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 476230 465.068 0.454 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 480730 469.463 0.458 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 486302 474.904 0.464 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 489102 477.639 0.466 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 493302 481.740 0.470 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 499602 487.893 0.476 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 502374 490.600 0.479 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 503774 491.967 0.480 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open ../atom_files/pdb1fas.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 514727 502.663 0.491 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 514803 502.737 0.491 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 514974 502.904 0.491 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 515824 503.734 0.492 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 517082 504.963 0.493 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 518986 506.822 0.495 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 519026 506.861 0.495 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 519116 506.949 0.495 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521972 509.738 0.498 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 522032 509.797 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 522167 509.929 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526451 514.112 0.502 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 526539 514.198 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 526737 514.392 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 533163 520.667 0.508 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 578891 565.323 0.552 read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 A 61 A 468 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 581192 567.570 0.554 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 616209 601.767 0.588 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 616922 602.463 0.588 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 651939 636.659 0.622 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 688297 672.165 0.656 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 700073 683.665 0.668 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 1 atom names : N -C CA H atom indices : 1 0 3 2 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 918 928 0 0 271 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 759197 741.403 0.724 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 805117 786.247 0.768 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 805273 786.399 0.768 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 61 920 930 1669 2455 271 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 805345 786.470 0.768 patch_______> segment topology patched using RTF: 61 ; TYR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 61 921 931 1671 2458 272 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 921 931 1671 2458 272 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 817209 798.056 0.779 patch_______> segment topology patched using RTF: 17 39 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 919 930 1671 2459 272 patch_______> segment topology patched using RTF: 3 22 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 917 929 1671 2460 272 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 817457 798.298 0.780 patch_______> segment topology patched using RTF: 53 59 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 915 928 1671 2461 272 patch_______> segment topology patched using RTF: 41 52 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 913 927 1671 2462 272 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 468 445 openf___224_> Open 1fas.ini1 wrgrasp_566_> Residues, atoms, charge: 61 913 4.0000 openf___224_> Open 1fas.ini2 wrpdb___568_> Residues, atoms, selected atoms: 61 913 913 Dynamically allocated memory at finish [B,KiB,MiB]: 744409 726.962 0.710 Starting time : 2016/04/05 22:41:50 Closing time : 2016/04/05 22:41:51 Total CPU time [seconds] : 0.34