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 toxin.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 257771 251.729 0.246 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 263134 256.967 0.251 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 278226 271.705 0.265 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 293626 286.744 0.280 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 293866 286.979 0.280 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 294146 287.252 0.281 Read the alignment from file : toxin.ali Total number of alignment positions: 75 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fas 61 1 1fas fasciculin 1 2 2ctx 71 1 2ctx alpha-cobratoxin align___276_> 'align_block' changed to 1. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Pairwise dynamic programming alignment (ALIGN): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -600.0000 Gap extension penalty : -400.0000 Break-break bonus : 10000.0000 Length of alignment : 71 Score : 26716.0000 openf___224_> Open ../atom_files/pdb1fas.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 314171 306.808 0.300 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 314171 306.808 0.300 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 314342 306.975 0.300 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 315192 307.805 0.301 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 316450 309.033 0.302 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 318354 310.893 0.304 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 318354 310.893 0.304 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 318444 310.980 0.304 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 321300 313.770 0.306 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 321300 313.770 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 321435 313.901 0.307 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 325719 318.085 0.311 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 325719 318.085 0.311 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 325917 318.278 0.311 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 332343 324.554 0.317 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 332289 324.501 0.317 openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 355314 346.986 0.339 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 355314 346.986 0.339 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 355485 347.153 0.339 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 356335 347.983 0.340 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357593 349.212 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 359497 351.071 0.343 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 359497 351.071 0.343 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 359587 351.159 0.343 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 362443 353.948 0.346 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 362443 353.948 0.346 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 362578 354.080 0.346 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 366862 358.264 0.350 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 366862 358.264 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367060 358.457 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 373486 364.732 0.356 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 373486 364.732 0.356 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 373783 365.022 0.356 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 373522 364.768 0.356 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 56 56 3.2757 3.2757 0.9113 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 56 56 2.7365 2.7365 0.0674 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 3 57 57 2.5174 2.5174 0.0314 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 4 58 58 2.5175 2.5175 0.0055 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 5 57 57 2.3344 2.3344 0.0163 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 6 57 57 2.3344 2.3344 0.0109 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 7 57 57 2.3344 2.3344 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Numb of residues/atoms in STR1 : 61 468 Numb of residues/atoms in STR2 : 71 518 Maximal distance for equivalence : 8.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 4.0000 Alignment score : 190.0543 Numb of aligned residues : 57 Numb of aligned atoms : 57 57 Numb of aligned atom-atom distanc: 1596 1596 RMS after superposition : 2.3344 2.3344 DRMS : 1.8807 1.8807 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 399559 390.194 0.381 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fas 2ctx # =============================== 1 1.469 0.000 T 1 I 1 2 1.057 0.000 M 2 R 2 3 0.831 0.000 * C 3 C 3 4 0.976 0.000 Y 4 F 4 5 1.204 0.000 S 5 I 5 6 1.118 0.000 H 6 T 6 7 1.685 0.000 T 7 P 7 8 2.049 0.000 T 8 D 8 # =============================== 9 0.898 0.000 S 10 I 9 10 1.709 0.000 R 11 T 10 11 2.604 0.000 A 12 S 11 12 1.579 0.000 I 13 K 12 13 1.578 0.000 L 14 D 13 14 1.036 0.000 T 15 C 14 15 1.600 0.000 N 16 P 15 16 2.051 0.000 C 17 N 16 17 2.536 0.000 * G 18 G 17 # =============================== 18 0.905 0.000 N 20 H 18 19 0.767 0.000 S 21 V 19 20 0.821 0.000 * C 22 C 20 21 0.664 0.000 * Y 23 Y 21 22 0.721 0.000 R 24 T 22 23 0.646 0.000 * K 25 K 23 24 0.904 0.000 S 26 T 24 25 0.617 0.000 R 27 W 25 # =============================== 26 1.623 0.000 H 29 C 26 # =============================== 27 1.280 0.000 P 30 C 30 # =============================== 28 1.424 0.000 P 31 G 34 29 0.382 0.000 * K 32 K 35 30 0.814 0.000 M 33 R 36 31 0.610 0.000 * V 34 V 37 32 1.171 0.000 L 35 D 38 33 1.789 0.000 G 36 L 39 34 0.693 0.000 R 37 G 40 35 0.914 0.000 G 38 C 41 36 0.688 0.000 C 39 A 42 # =============================== 37 1.326 0.000 G 40 T 44 38 0.704 0.000 * C 41 C 45 39 0.562 0.000 * P 42 P 46 40 0.693 0.000 P 43 T 47 41 0.900 0.000 G 44 V 48 42 1.612 0.000 D 45 K 49 43 1.510 0.000 D 46 T 50 44 1.287 0.000 Y 47 G 51 45 0.629 0.000 L 48 V 52 46 0.508 0.000 E 49 D 53 47 0.576 0.000 V 50 I 54 48 0.289 0.000 K 51 Q 55 49 0.327 0.000 * C 52 C 56 50 0.341 0.000 * C 53 C 57 51 0.692 0.000 T 54 S 58 52 0.929 0.000 S 55 T 59 # =============================== 53 0.267 0.000 * D 57 D 60 54 0.446 0.000 K 58 N 61 55 0.439 0.000 * C 59 C 62 56 0.791 0.000 * N 60 N 63 57 0.785 0.000 Y 61 P 64 # =============================== openf___224_> Open toxin-str.ali openf___224_> Open ../atom_files/pdb1fas.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 265684 259.457 0.253 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 265760 259.531 0.253 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 265931 259.698 0.254 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 266781 260.528 0.254 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 268039 261.757 0.256 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 269943 263.616 0.257 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 269983 263.655 0.257 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 270073 263.743 0.258 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 272929 266.532 0.260 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 272989 266.591 0.260 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 273124 266.723 0.260 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 277408 270.906 0.265 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 277496 270.992 0.265 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 277694 271.186 0.265 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 284120 277.461 0.271 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 329848 322.117 0.315 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]: 331588 323.816 0.316 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 366605 358.013 0.350 openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 366737 358.142 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367034 358.432 0.350 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 371786 363.072 0.355 read_mo_297_> Segments, residues, atoms: 1 71 518 read_mo_298_> Segment: 1 1 A 71 A 518 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 372879 364.140 0.356 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 412726 403.053 0.394 align___276_> 'align_block' changed to 1. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Pairwise dynamic programming alignment (ALIGN): Residue-residue metric : $(LIB)/as1.sim.mat Diagonal : 100 Overhang : 0 Local alignment : F MATRIX_OFFSET (local aln): 0.0000 N_SUBOPT : 0 SUBOPT_OFFSET : 0.0000 Alignment block : 1 Gap introduction penalty : -600.0000 Gap extension penalty : -400.0000 Break-break bonus : 10000.0000 Length of alignment : 71 Score : 26716.0000 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 413828 404.129 0.395 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 1 32 32 2.2868 2.2868 0.9429 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 2 42 42 2.4575 2.4575 0.0289 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 3 45 46 2.2939 2.3606 0.0255 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 4 46 47 2.0828 2.1417 0.0210 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 5 50 51 1.8530 1.9235 0.0175 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 6 51 51 1.7372 1.7372 0.0375 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 7 51 51 1.7279 1.7279 0.0205 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 8 51 51 1.7279 1.7279 0.0007 inialig_318_> I,NEQVCUT,NEQV,RMSCUT,RMS,RMSROT: 9 51 51 1.7279 1.7279 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Numb of residues/atoms in STR1 : 61 468 Numb of residues/atoms in STR2 : 71 518 Maximal distance for equivalence : 4.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 2.0000 Alignment score : 137.3289 Numb of aligned residues : 51 Numb of aligned atoms : 51 51 Numb of aligned atom-atom distanc: 1263 1275 RMS after superposition : 1.7279 1.7279 DRMS : 1.2507 1.3111 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 414892 405.168 0.396 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 443011 432.628 0.422 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 1fas 2ctx # =============================== 1 1.157 0.000 T 1 I 1 2 0.461 0.000 M 2 R 2 3 0.281 0.000 * C 3 C 3 4 0.461 0.000 Y 4 F 4 5 0.660 0.000 S 5 I 5 6 0.669 0.000 H 6 T 6 7 1.718 0.000 T 7 P 7 # =============================== 8 1.199 0.000 T 9 I 9 # =============================== 9 1.623 0.000 A 12 T 10 # =============================== 10 0.402 0.000 L 14 K 12 11 1.470 0.000 T 15 D 13 12 1.037 0.000 N 16 C 14 # =============================== 13 1.551 0.000 C 17 G 17 # =============================== 14 0.444 0.000 N 20 H 18 15 0.278 0.000 S 21 V 19 16 0.429 0.000 * C 22 C 20 17 0.358 0.000 * Y 23 Y 21 18 0.542 0.000 R 24 T 22 19 0.575 0.000 * K 25 K 23 20 0.793 0.000 S 26 T 24 21 0.567 0.000 R 27 W 25 # =============================== 22 1.804 0.000 H 29 C 26 # =============================== 23 1.262 0.000 P 30 C 30 # =============================== 24 1.427 0.000 P 31 G 34 25 0.216 0.000 * K 32 K 35 26 0.823 0.000 M 33 R 36 27 0.570 0.000 * V 34 V 37 # =============================== 28 1.046 0.000 G 36 D 38 29 0.855 0.000 R 37 L 39 30 0.848 0.000 * G 38 G 40 31 0.939 0.000 * C 39 C 41 32 0.961 0.000 G 40 A 42 # =============================== 33 1.014 0.000 * C 41 C 45 34 0.732 0.000 * P 42 P 46 35 0.788 0.000 P 43 T 47 36 1.033 0.000 G 44 V 48 # =============================== 37 1.223 0.000 D 45 T 50 38 0.697 0.000 D 46 G 51 # =============================== 39 0.584 0.000 L 48 V 52 40 0.558 0.000 E 49 D 53 41 0.593 0.000 V 50 I 54 42 0.317 0.000 K 51 Q 55 43 0.276 0.000 * C 52 C 56 44 0.224 0.000 * C 53 C 57 45 0.353 0.000 T 54 S 58 46 0.642 0.000 S 55 T 59 # =============================== 47 0.642 0.000 * D 57 D 60 48 0.493 0.000 K 58 N 61 49 0.216 0.000 * C 59 C 62 50 0.437 0.000 * N 60 N 63 51 0.416 0.000 Y 61 P 64 # =============================== openf___224_> Open toxin-str.ali openf___224_> Open ../atom_files/pdb1fas.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453964 443.324 0.433 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 454040 443.398 0.433 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 454211 443.565 0.433 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 455061 444.396 0.434 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 456319 445.624 0.435 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 458223 447.483 0.437 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 458263 447.522 0.437 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 458353 447.610 0.437 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461209 450.399 0.440 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 461269 450.458 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 461404 450.590 0.440 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465688 454.773 0.444 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 465776 454.859 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465974 455.053 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 472400 461.328 0.451 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 518128 505.984 0.494 read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 A 61 A 468 openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 448783 438.265 0.428 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 448859 438.339 0.428 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449030 438.506 0.428 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449880 439.336 0.429 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 451138 440.564 0.430 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453042 442.424 0.432 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 453082 442.463 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 453172 442.551 0.432 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 456028 445.340 0.435 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 456088 445.398 0.435 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 456223 445.530 0.435 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460507 449.714 0.439 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 460595 449.800 0.439 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 460793 449.993 0.439 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 467219 456.269 0.446 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 467351 456.397 0.446 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 467648 456.688 0.446 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 518128 505.984 0.494 read_mo_297_> Segments, residues, atoms: 1 71 518 read_mo_298_> Segment: 1 1 A 71 A 518 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): # ALGNMT CODE 1 1fas 2 2ctx 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 : 61 Numb of atoms/sel atoms in MODEL : 468 61 Numb of residues in MODEL2 : 71 Numb of atoms in MODEL2 : 518 Equivalences refinement : F Numb of aligned equiv positions : 51 Numb of aligned equiv distances : 1275 RMS before superposition : 33.3208 RMS after superposition : 1.7279 DRMS : 1.3111 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 50 Numb of equiv cutoff distances : 1250 Cutoff RMS after superposition : 1.6688 Cutoff DRMS : 1.1986 X_new = Rotation * X + Translation Rotation matrix : -0.6609 -0.5094 0.5510 0.0275 -0.7502 -0.6606 0.7499 -0.4214 0.5099 Translation vector: 66.6448 58.3884 8.3890 Dynamically allocated memory at finish [B,KiB,MiB]: 518128 505.984 0.494 Starting time : 2016/04/05 22:41:50 Closing time : 2016/04/05 22:41:50 Total CPU time [seconds] : 0.21