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 22:41:49 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_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open toxin.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 393839 384.608 0.376 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 395260 385.996 0.377 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 396710 387.412 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 396990 387.686 0.379 Read the alignment from file : toxin.ali Total number of alignment positions: 71 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin openf___224_> Open toxin.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 429974 419.896 0.410 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 430234 420.150 0.410 Read the alignment from file : toxin.ali Total number of alignment positions: 71 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2nbt 66 1 2nbt neuronal bungarotoxin openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453259 442.636 0.432 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 453259 442.636 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453430 442.803 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 454280 443.633 0.433 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 455538 444.861 0.434 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 457442 446.721 0.436 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 457442 446.721 0.436 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 457532 446.809 0.436 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460388 449.598 0.439 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 460388 449.598 0.439 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460523 449.729 0.439 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 464807 453.913 0.443 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 464807 453.913 0.443 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465005 454.106 0.443 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 471431 460.382 0.450 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 471431 460.382 0.450 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 471728 460.672 0.450 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 471467 460.417 0.450 openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Pairwise dynamic programming alignment (ALIGN2D): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Maximal gap length : 999999 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -100.0000 Gap extension penalty : 0.0000 Gap diagonal penalty : 0.0000 Structure gap penalties : 3.500 3.500 3.500 0.200 4.000 6.500 2.000 0.000 Break-break bonus : 10000.0000 Length of alignment : 73 Score : 44261.7852 openf___224_> Open align2d.ali openf___224_> Open align2d.pap check_a_343_> >> BEGINNING OF COMMAND check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open align2d.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 393839 384.608 0.376 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 395260 385.996 0.377 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 396710 387.412 0.378 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 429694 419.623 0.410 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 429974 419.896 0.410 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 430234 420.150 0.410 Read the alignment from file : align2d.ali Total number of alignment positions: 73 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2nbt 66 1 2nbt neuronal bungarotoxin openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 441187 430.847 0.421 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 441263 430.921 0.421 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 441434 431.088 0.421 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 442284 431.918 0.422 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 443542 433.146 0.423 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 445446 435.006 0.425 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 445486 435.045 0.425 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 445576 435.133 0.425 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 448432 437.922 0.428 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 448492 437.980 0.428 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 448627 438.112 0.428 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 452911 442.296 0.432 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 452999 442.382 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453197 442.575 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 459623 448.851 0.438 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 459755 448.979 0.438 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460052 449.270 0.439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 510532 498.566 0.487 read_mo_297_> Segments, residues, atoms: 1 71 518 read_mo_298_> Segment: 1 1 A 71 A 518 openf___224_> Open 2ctx.aln.pdb wrpdb___568_> Residues, atoms, selected atoms: 71 518 518 openf___224_> Open 2ctx.ssm openf___224_> Open 2ctx.ssm.pdb wrpdb___568_> Residues, atoms, selected atoms: 71 518 518 openf___224_> Open ../atom_files/2nbt.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521485 509.263 0.497 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 521561 509.337 0.497 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 521732 509.504 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 522582 510.334 0.498 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 523840 511.562 0.500 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 525744 513.422 0.501 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 525784 513.461 0.501 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 525874 513.549 0.502 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 528730 516.338 0.504 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 528790 516.396 0.504 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 528925 516.528 0.504 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 533209 520.712 0.509 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 533297 520.798 0.509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 533495 520.991 0.509 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 539921 527.267 0.515 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 585649 571.923 0.559 read_mo_297_> Segments, residues, atoms: 1 66 501 read_mo_298_> Segment: 1 1 A 66 A 501 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 2ctx 2 2nbt Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 71 Numb of atoms/sel atoms in MODEL : 518 71 Numb of residues in MODEL2 : 66 Numb of atoms in MODEL2 : 501 Equivalences refinement : F Numb of aligned equiv positions : 64 Numb of aligned equiv distances : 2016 RMS before superposition : 57.8500 RMS after superposition : 6.2260 DRMS : 3.9907 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 25 Numb of equiv cutoff distances : 1526 Cutoff RMS after superposition : 2.1387 Cutoff DRMS : 1.5679 X_new = Rotation * X + Translation Rotation matrix : 0.9952 -0.0361 -0.0907 -0.0811 0.2131 -0.9737 0.0545 0.9764 0.2091 Translation vector: 23.6670 44.9946 14.2224 openf___224_> Open 2nbt.fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 66 501 501 Dynamically allocated memory at finish [B,KiB,MiB]: 585649 571.923 0.559 Starting time : 2016/04/05 22:41:49 Closing time : 2016/04/05 22:41:50 Total CPU time [seconds] : 0.40