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 22:38:48 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 alignment.seg Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269381 263.067 0.257 openf___224_> Open ../atom_files/pdb1fdn.ent Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 278929 272.392 0.266 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 288477 281.716 0.275 openf___224_> Open ../atom_files/pdb5fd1.ent openf___224_> Open ../atom_files/pdb1fxd.ent openf___224_> Open ../atom_files/pdb1iqz.ent Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 288713 281.946 0.275 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 288929 282.157 0.276 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 289153 282.376 0.276 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 289389 282.606 0.276 Read the alignment from file : alignment.seg Total number of alignment positions: 60 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 60 1 5fd1 ferredoxin 2 1fdn 55 1 1fdn ferredoxin 3 1fxd 57 1 1fxd ferredoxin 4 1iqz 60 1 1iqz ferredoxin openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 289697 282.907 0.276 Multiple dynamic programming alignment (MALIGN): Residue-residue metric : $(LIB)/as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 64 openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 309422 302.170 0.295 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 309422 302.170 0.295 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 309593 302.337 0.295 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 310443 303.167 0.296 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 311701 304.396 0.297 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 313605 306.255 0.299 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 313605 306.255 0.299 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 313695 306.343 0.299 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 316551 309.132 0.302 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 316551 309.132 0.302 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 316686 309.264 0.302 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 320970 313.447 0.306 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 320970 313.447 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 321168 313.641 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 327594 319.916 0.312 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 327531 319.854 0.312 openf___224_> Open ../atom_files/pdb1fdn.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 345756 337.652 0.330 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 345756 337.652 0.330 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 345927 337.819 0.330 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 346777 338.649 0.331 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 348035 339.878 0.332 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 349939 341.737 0.334 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 349939 341.737 0.334 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 350029 341.825 0.334 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 352885 344.614 0.337 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 352885 344.614 0.337 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 353020 344.746 0.337 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357304 348.930 0.341 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 357304 348.930 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357502 349.123 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 363928 355.398 0.347 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 363820 355.293 0.347 openf___224_> Open ../atom_files/pdb1fxd.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 382645 373.677 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 382645 373.677 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 382816 373.844 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383666 374.674 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 384924 375.902 0.367 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 386828 377.762 0.369 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 386828 377.762 0.369 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 386918 377.850 0.369 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 389774 380.639 0.372 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 389774 380.639 0.372 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 389909 380.771 0.372 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 394193 384.954 0.376 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 394193 384.954 0.376 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 394391 385.147 0.376 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 400817 391.423 0.382 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 400727 391.335 0.382 openf___224_> Open ../atom_files/pdb1iqz.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 420452 410.598 0.401 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 420452 410.598 0.401 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 420623 410.765 0.401 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 421473 411.595 0.402 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 422731 412.823 0.403 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 424635 414.683 0.405 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 424635 414.683 0.405 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 424725 414.771 0.405 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 427581 417.560 0.408 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 427581 417.560 0.408 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 427716 417.691 0.408 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 432000 421.875 0.412 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 432000 421.875 0.412 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 432198 422.068 0.412 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 438624 428.344 0.418 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 438561 428.282 0.418 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 460781 449.981 0.439 malign3_328_> Initial framework positions: 60 malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 1 8 0.0000 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 462013 451.185 0.441 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 463401 452.540 0.442 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 472333 461.263 0.450 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 482396 471.090 0.460 malign3_332_> Framework: 1 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 1.348 0.603 F 2 Y 2 I 2 T 4 2 0.672 0.324 V 3 V 3 E 3 I 5 3 1.055 0.619 V 4 I 4 V 4 V 6 # ============================================= 4 1.395 0.652 K 12 S 10 A 10 G 15 # ============================================= 5 0.960 0.422 T 14 G 12 E 12 G 18 6 1.150 0.654 D 15 A 13 A 13 A 19 # ============================================= 7 1.179 0.582 C 16 C 14 C 14 A 21 # ============================================= 8 1.270 0.575 E 18 P 16 E 16 P 22 9 0.941 0.313 V 19 E 17 I 17 D 23 # ============================================= 10 1.719 0.769 F 25 I 23 F 22 Y 25 11 1.796 0.845 Y 26 S 24 E 23 D 26 12 1.164 0.174 E 27 S 25 M 24 Y 27 # ============================================= 13 0.795 0.263 L 32 Y 30 A 31 A 33 14 0.821 0.145 V 33 V 31 V 32 Y 34 15 0.887 0.556 I 34 I 32 V 33 V 35 # ============================================= 16 0.746 0.232 H 35 D 33 I 34 D 39 # ============================================= 17 1.222 0.372 P 36 A 34 P 36 Q 41 # ============================================= 18 1.605 0.641 I 40 I 38 S 38 V 44 19 1.854 0.646 D 41 D 39 D 39 E 45 # ============================================= 20 1.504 0.698 A 43 G 41 E 44 P 47 # ============================================= 21 1.113 0.236 L 44 A 42 E 45 L 50 # ============================================= 22 1.134 0.336 P 47 G 45 D 48 D 52 23 0.922 0.159 E 48 V 46 S 49 D 53 # ============================================= 24 0.904 0.345 C 49 C 47 C 50 A 57 # ============================================= 25 0.983 0.310 Q 52 D 50 E 53 F 58 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 2 4 0.0000 malign3_332_> Framework: 2 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.999 0.351 F 2 Y 2 I 2 T 4 2 0.597 0.250 V 3 V 3 E 3 I 5 3 1.042 0.512 V 4 I 4 V 4 V 6 # ============================================= 4 0.890 0.495 K 12 S 10 A 10 G 15 # ============================================= 5 0.629 0.418 T 14 G 12 E 12 G 18 6 0.987 0.657 D 15 A 13 A 13 A 19 # ============================================= 7 0.806 0.514 C 16 C 14 C 14 A 21 8 1.053 0.443 V 17 E 15 V 15 P 22 # ============================================= 9 1.081 0.574 V 19 E 17 I 17 D 23 10 1.487 0.800 C 20 C 18 C 18 I 24 # ============================================= 11 1.433 0.729 F 25 I 23 F 22 Y 25 12 1.299 0.871 Y 26 S 24 E 23 D 26 13 0.679 0.238 E 27 S 25 M 24 Y 27 14 1.473 0.776 G 28 G 26 N 25 D 28 # ============================================= 15 1.576 0.774 F 31 R 29 K 30 I 32 16 0.611 0.280 L 32 Y 30 A 31 A 33 17 0.483 0.203 V 33 V 31 V 32 Y 34 18 0.703 0.490 I 34 I 32 V 33 V 35 # ============================================= 19 0.686 0.231 H 35 D 33 I 34 D 39 # ============================================= 20 1.188 0.349 P 36 A 34 P 36 Q 41 # ============================================= 21 1.343 0.632 I 40 I 38 D 39 V 44 # ============================================= 22 1.460 0.293 C 42 C 40 D 41 P 47 # ============================================= 23 0.965 0.080 L 44 A 42 E 45 L 50 # ============================================= 24 0.892 0.364 P 47 G 45 D 48 D 52 25 0.636 0.296 E 48 V 46 S 49 D 53 # ============================================= 26 0.730 0.366 C 49 C 47 C 50 A 57 # ============================================= 27 0.766 0.299 A 51 V 49 A 52 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 3 3 0.0000 malign3_332_> Framework: 3 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.961 0.448 F 2 Y 2 I 2 T 4 2 0.646 0.323 V 3 V 3 E 3 I 5 3 0.958 0.437 V 4 I 4 V 4 V 6 # ============================================= 4 0.661 0.315 K 12 S 10 A 10 G 15 # ============================================= 5 0.687 0.456 T 14 G 12 E 12 G 18 6 0.980 0.534 D 15 A 13 A 13 A 19 # ============================================= 7 0.872 0.471 C 16 C 14 C 14 A 21 8 1.055 0.402 V 17 E 15 V 15 P 22 # ============================================= 9 1.005 0.407 C 20 C 18 C 18 D 23 # ============================================= 10 1.411 0.753 F 25 I 23 F 22 Y 25 11 1.321 0.855 Y 26 S 24 E 23 D 26 12 0.669 0.234 E 27 S 25 M 24 Y 27 13 1.155 0.586 G 28 G 26 N 25 D 28 # ============================================= 14 1.818 0.448 P 29 D 27 E 27 D 30 # ============================================= 15 1.301 0.637 F 31 R 29 K 30 I 32 16 0.532 0.260 L 32 Y 30 A 31 A 33 17 0.470 0.241 V 33 V 31 V 32 Y 34 18 0.731 0.495 I 34 I 32 V 33 V 35 # ============================================= 19 0.745 0.228 H 35 D 33 I 34 D 39 # ============================================= 20 1.105 0.310 P 36 A 34 P 36 Q 41 # ============================================= 21 1.202 0.564 I 40 I 38 D 39 V 44 # ============================================= 22 1.472 0.358 C 42 C 40 D 41 P 47 # ============================================= 23 0.988 0.240 L 44 A 42 E 45 L 50 # ============================================= 24 0.572 0.230 E 46 A 44 I 47 M 54 25 1.139 0.620 P 47 G 45 D 48 M 55 26 1.382 0.789 E 48 V 46 S 49 D 56 27 0.601 0.287 C 49 C 47 C 50 A 57 # ============================================= 28 0.656 0.126 A 51 V 49 A 52 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 4 3 0.0000 malign3_332_> Framework: 4 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.973 0.425 F 2 Y 2 I 2 T 4 2 0.650 0.218 V 3 V 3 E 3 I 5 3 0.812 0.339 V 4 I 4 V 4 V 6 4 1.409 0.755 T 5 N 5 N 5 D 7 # ============================================= 5 1.340 0.662 D 6 E 6 D 6 T 10 # ============================================= 6 1.267 0.500 C 11 I 9 M 9 C 14 7 0.667 0.356 K 12 S 10 A 10 G 15 # ============================================= 8 0.800 0.480 T 14 G 12 E 12 G 18 9 0.851 0.461 D 15 A 13 A 13 A 19 # ============================================= 10 0.898 0.398 C 16 C 14 C 14 A 21 11 0.944 0.349 V 17 E 15 V 15 P 22 # ============================================= 12 0.916 0.347 C 20 C 18 C 18 D 23 # ============================================= 13 1.335 0.707 F 25 I 23 F 22 Y 25 14 1.304 0.799 Y 26 S 24 E 23 D 26 15 0.790 0.207 E 27 S 25 M 24 Y 27 16 0.959 0.459 G 28 G 26 N 25 D 28 # ============================================= 17 1.530 0.421 P 29 D 27 E 27 D 30 # ============================================= 18 1.052 0.558 F 31 R 29 K 30 I 32 19 0.556 0.207 L 32 Y 30 A 31 A 33 20 0.498 0.145 V 33 V 31 V 32 Y 34 21 0.680 0.430 I 34 I 32 V 33 V 35 22 1.649 0.804 H 35 D 33 I 34 T 36 # ============================================= 23 1.330 0.384 P 36 A 34 P 36 Q 41 # ============================================= 24 1.444 0.412 C 39 C 37 S 38 V 44 25 1.364 0.445 I 40 I 38 D 39 E 45 # ============================================= 26 1.553 0.435 C 42 C 40 D 41 P 47 # ============================================= 27 1.231 0.472 L 44 A 42 E 45 I 51 # ============================================= 28 1.497 0.871 C 45 C 43 A 46 D 53 29 0.763 0.402 E 46 A 44 I 47 M 54 30 0.866 0.420 P 47 G 45 D 48 M 55 31 1.034 0.601 E 48 V 46 S 49 D 56 32 0.473 0.201 C 49 C 47 C 50 A 57 # ============================================= 33 0.908 0.267 A 51 V 49 A 52 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 5 3 0.0000 malign3_332_> Framework: 5 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.890 0.445 F 2 Y 2 I 2 T 4 2 0.599 0.216 V 3 V 3 E 3 I 5 3 0.737 0.297 V 4 I 4 V 4 V 6 4 1.213 0.627 T 5 N 5 N 5 D 7 # ============================================= 5 1.105 0.523 D 6 E 6 D 6 T 10 # ============================================= 6 1.126 0.373 C 11 I 9 M 9 C 14 7 0.674 0.358 K 12 S 10 A 10 G 15 # ============================================= 8 0.842 0.467 T 14 G 12 E 12 G 18 9 0.850 0.456 D 15 A 13 A 13 A 19 # ============================================= 10 0.897 0.336 C 16 C 14 C 14 A 21 11 0.845 0.285 V 17 E 15 V 15 P 22 # ============================================= 12 1.017 0.502 C 20 C 18 C 18 D 23 # ============================================= 13 1.262 0.668 F 25 I 23 F 22 Y 25 14 1.307 0.739 Y 26 S 24 E 23 D 26 15 0.904 0.209 E 27 S 25 M 24 Y 27 16 0.817 0.301 G 28 G 26 N 25 D 28 # ============================================= 17 1.522 0.448 P 29 D 27 E 27 D 30 # ============================================= 18 0.917 0.471 F 31 R 29 K 30 I 32 19 0.630 0.251 L 32 Y 30 A 31 A 33 20 0.509 0.147 V 33 V 31 V 32 Y 34 21 0.601 0.344 I 34 I 32 V 33 V 35 22 1.518 0.694 H 35 D 33 I 34 T 36 # ============================================= 23 1.462 0.529 P 36 A 34 P 36 Q 41 # ============================================= 24 1.388 0.370 C 39 C 37 S 38 V 44 25 1.145 0.311 I 40 I 38 D 39 E 45 # ============================================= 26 1.780 0.448 C 42 C 40 D 41 P 47 # ============================================= 27 1.101 0.509 L 44 A 42 E 45 I 51 # ============================================= 28 0.823 0.338 C 45 C 43 A 46 M 54 # ============================================= 29 0.720 0.344 P 47 G 45 D 48 M 55 30 0.744 0.463 E 48 V 46 S 49 D 56 31 0.540 0.247 C 49 C 47 C 50 A 57 # ============================================= 32 0.748 0.416 P 50 P 48 P 51 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 6 3 0.0000 malign3_332_> Framework: 6 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.977 0.511 F 2 Y 2 I 2 T 4 2 0.647 0.241 V 3 V 3 E 3 I 5 3 0.610 0.186 V 4 I 4 V 4 V 6 4 1.018 0.511 T 5 N 5 N 5 D 7 # ============================================= 5 0.931 0.404 D 6 E 6 D 6 T 10 # ============================================= 6 1.150 0.386 C 11 I 9 M 9 C 14 7 0.779 0.428 K 12 S 10 A 10 G 15 # ============================================= 8 0.871 0.453 T 14 G 12 E 12 G 18 # ============================================= 9 0.874 0.392 D 15 A 13 A 13 A 20 10 0.990 0.393 C 16 C 14 C 14 A 21 11 0.891 0.301 V 17 E 15 V 15 P 22 # ============================================= 12 1.230 0.649 F 25 I 23 F 22 Y 25 13 1.280 0.736 Y 26 S 24 E 23 D 26 14 0.897 0.220 E 27 S 25 M 24 Y 27 15 0.794 0.285 G 28 G 26 N 25 D 28 # ============================================= 16 1.528 0.440 P 29 D 27 E 27 D 30 # ============================================= 17 0.839 0.410 F 31 R 29 K 30 I 32 18 0.585 0.214 L 32 Y 30 A 31 A 33 19 0.533 0.164 V 33 V 31 V 32 Y 34 20 0.635 0.383 I 34 I 32 V 33 V 35 21 1.514 0.692 H 35 D 33 I 34 T 36 # ============================================= 22 1.446 0.511 P 36 A 34 P 36 Q 41 # ============================================= 23 1.365 0.350 C 39 C 37 S 38 V 44 24 1.087 0.253 I 40 I 38 D 39 E 45 # ============================================= 25 2.116 0.637 C 42 C 40 D 41 D 48 # ============================================= 26 1.081 0.491 L 44 A 42 E 45 I 51 # ============================================= 27 0.738 0.319 C 45 C 43 A 46 M 54 # ============================================= 28 0.576 0.256 P 47 G 45 D 48 M 55 29 0.556 0.348 E 48 V 46 S 49 D 56 30 0.584 0.264 C 49 C 47 C 50 A 57 # ============================================= 31 0.567 0.287 P 50 P 48 P 51 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 7 3 0.0000 malign3_332_> Framework: 7 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.956 0.496 F 2 Y 2 I 2 T 4 2 0.642 0.248 V 3 V 3 E 3 I 5 3 0.621 0.197 V 4 I 4 V 4 V 6 4 1.006 0.502 T 5 N 5 N 5 D 7 # ============================================= 5 0.925 0.404 D 6 E 6 D 6 T 10 # ============================================= 6 1.172 0.426 C 11 I 9 M 9 C 14 7 0.784 0.433 K 12 S 10 A 10 G 15 # ============================================= 8 0.863 0.415 T 14 G 12 E 12 G 18 # ============================================= 9 0.760 0.284 D 15 A 13 A 13 A 20 10 0.980 0.382 C 16 C 14 C 14 A 21 11 0.893 0.316 V 17 E 15 V 15 P 22 # ============================================= 12 1.187 0.608 F 25 I 23 F 22 Y 25 13 1.266 0.679 Y 26 S 24 E 23 D 26 14 0.960 0.220 E 27 S 25 M 24 Y 27 15 0.843 0.281 G 28 G 26 N 25 D 28 # ============================================= 16 1.627 0.366 P 29 D 27 E 27 D 30 # ============================================= 17 1.617 0.602 N 30 D 28 D 29 G 31 18 0.894 0.446 F 31 R 29 K 30 I 32 19 0.634 0.264 L 32 Y 30 A 31 A 33 20 0.512 0.154 V 33 V 31 V 32 Y 34 21 0.615 0.330 I 34 I 32 V 33 V 35 22 1.490 0.681 H 35 D 33 I 34 T 36 # ============================================= 23 1.470 0.541 P 36 A 34 P 36 Q 41 # ============================================= 24 1.306 0.292 C 39 C 37 S 38 V 44 25 0.960 0.197 I 40 I 38 D 39 E 45 # ============================================= 26 2.123 0.665 C 42 C 40 D 41 D 48 # ============================================= 27 1.037 0.447 L 44 A 42 E 45 I 51 # ============================================= 28 0.641 0.222 C 45 C 43 A 46 M 54 # ============================================= 29 0.600 0.253 P 47 G 45 D 48 M 55 30 0.416 0.225 E 48 V 46 S 49 D 56 31 0.644 0.305 C 49 C 47 C 50 A 57 # ============================================= 32 0.515 0.225 P 50 P 48 P 51 G 60 # ============================================= malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 8 3 0.0000 malign3_332_> Framework: 8 # 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 5fd1 1fdn 1fxd 1iqz # ============================================= 1 0.969 0.482 F 2 Y 2 I 2 T 4 2 0.664 0.219 V 3 V 3 E 3 I 5 3 0.625 0.187 V 4 I 4 V 4 V 6 4 0.999 0.482 T 5 N 5 N 5 D 7 # ============================================= 5 0.931 0.417 D 6 E 6 D 6 T 10 # ============================================= 6 1.110 0.392 C 11 I 9 M 9 C 14 7 0.739 0.429 K 12 S 10 A 10 G 15 # ============================================= 8 0.856 0.394 T 14 G 12 E 12 G 18 # ============================================= 9 0.762 0.282 D 15 A 13 A 13 A 20 10 0.976 0.390 C 16 C 14 C 14 A 21 11 0.880 0.357 V 17 E 15 V 15 P 22 # ============================================= 12 1.218 0.617 F 25 I 23 F 22 Y 25 13 1.315 0.684 Y 26 S 24 E 23 D 26 14 1.016 0.282 E 27 S 25 M 24 Y 27 15 0.829 0.272 G 28 G 26 N 25 D 28 # ============================================= 16 1.579 0.295 P 29 D 27 E 27 D 30 # ============================================= 17 1.470 0.540 N 30 D 28 D 29 G 31 18 0.847 0.450 F 31 R 29 K 30 I 32 19 0.680 0.281 L 32 Y 30 A 31 A 33 20 0.562 0.120 V 33 V 31 V 32 Y 34 21 0.621 0.343 I 34 I 32 V 33 V 35 22 1.482 0.694 H 35 D 33 I 34 T 36 # ============================================= 23 1.488 0.539 P 36 A 34 P 36 Q 41 # ============================================= 24 1.306 0.270 C 39 C 37 S 38 V 44 25 0.966 0.175 I 40 I 38 D 39 E 45 # ============================================= 26 2.158 0.693 C 42 C 40 D 41 D 48 # ============================================= 27 1.050 0.463 L 44 A 42 E 45 I 51 # ============================================= 28 0.643 0.219 C 45 C 43 A 46 M 54 # ============================================= 29 0.593 0.268 P 47 G 45 D 48 M 55 30 0.424 0.227 E 48 V 46 S 49 D 56 31 0.647 0.297 C 49 C 47 C 50 A 57 # ============================================= 32 0.554 0.226 P 50 P 48 P 51 G 60 # ============================================= Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 4.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 2.0000 Numb of residues in framework : 32 openf___224_> Open alignment.seg Read the alignment from file : alignment.seg Total number of alignment positions: 87 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 60 1 5fd1 ferredoxin 2 1fdn 55 1 1fdn ferredoxin 3 1fxd 57 1 1fxd ferredoxin 4 1iqz 60 1 1iqz ferredoxin 5 1fdx 54 1 ferredoxin 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 : 4 Gap introduction penalty : -600.0000 Gap extension penalty : -400.0000 Break-break bonus : 10000.0000 Length of alignment : 87 Score : 7810.5000 openf___224_> Open alignment.seg.ali Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 5fd1 @11fdn @11fxd @11iqz @21fdx @1 5fd1 @1 60 19 16 3 19 1fdn @1 35 55 11 3 29 1fxd @1 28 20 57 6 8 1iqz @2 5 5 11 60 6 1fdx @1 35 54 15 11 54 openf___224_> Open alignment.seg.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265439 259.218 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266889 260.634 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 299873 292.845 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300109 293.075 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300325 293.286 0.286 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300549 293.505 0.287 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300785 293.735 0.287 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 300997 293.942 0.287 Read the alignment from file : alignment.seg.ali Total number of alignment positions: 87 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 60 1 5fd1 ferredoxin 2 1fdn 55 1 1fdn ferredoxin 3 1fxd 57 1 1fxd ferredoxin 4 1iqz 60 1 1iqz ferredoxin 5 1fdx 54 1 ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 320722 313.205 0.306 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 320722 313.205 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 320893 313.372 0.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 321743 314.202 0.307 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 323001 315.431 0.308 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 324905 317.290 0.310 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 324905 317.290 0.310 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 324995 317.378 0.310 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 327851 320.167 0.313 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 327851 320.167 0.313 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 327986 320.299 0.313 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 332270 324.482 0.317 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 332270 324.482 0.317 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 332468 324.676 0.317 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 338894 330.951 0.323 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 338831 330.890 0.323 openf___224_> Open ../atom_files/pdb1fdn.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357056 348.688 0.341 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 357056 348.688 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 357227 348.854 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 358077 349.685 0.341 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 359335 350.913 0.343 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 361239 352.772 0.345 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 361239 352.772 0.345 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 361329 352.860 0.345 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 364185 355.649 0.347 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 364185 355.649 0.347 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 364320 355.781 0.347 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 368604 359.965 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 368604 359.965 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 368802 360.158 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 375228 366.434 0.358 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 375120 366.328 0.358 openf___224_> Open ../atom_files/pdb1fxd.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393945 384.712 0.376 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393945 384.712 0.376 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 394116 384.879 0.376 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 394966 385.709 0.377 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 396224 386.938 0.378 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 398128 388.797 0.380 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 398128 388.797 0.380 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 398218 388.885 0.380 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 401074 391.674 0.382 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 401074 391.674 0.382 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 401209 391.806 0.383 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 405493 395.989 0.387 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 405493 395.989 0.387 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 405691 396.183 0.387 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 412117 402.458 0.393 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 412027 402.370 0.393 openf___224_> Open ../atom_files/pdb1iqz.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 431752 421.633 0.412 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 431752 421.633 0.412 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 431923 421.800 0.412 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 432773 422.630 0.413 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 434031 423.858 0.414 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 435935 425.718 0.416 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 435935 425.718 0.416 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 436025 425.806 0.416 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 438881 428.595 0.419 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 438881 428.595 0.419 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 439016 428.727 0.419 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 443300 432.910 0.423 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 443300 432.910 0.423 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 443498 433.104 0.423 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 449924 439.379 0.429 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 449861 439.317 0.429 check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- END OF TABLE 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 ---------------------------------------------- 18 1 12 15 G A 8.487 18 2 10 13 G A 8.284 18 3 10 13 G A 8.347 18 4 15 20 G A 9.282 37 1 27 30 G S 8.148 37 2 25 28 G S 8.647 47 3 34 37 D A 9.206 47 4 36 43 D A 11.135 58 1 40 43 I D 8.285 58 2 38 41 I D 8.601 58 3 39 44 I D 9.058 END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 589113 575.306 0.562 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 590713 576.868 0.563 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 594693 580.755 0.567 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 596693 582.708 0.569 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 599693 585.638 0.572 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 604193 590.032 0.576 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 609765 595.474 0.582 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 612565 598.208 0.584 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 616765 602.310 0.588 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 623065 608.462 0.594 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 625837 611.169 0.597 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 627237 612.536 0.598 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 635558 620.662 0.606 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 673876 658.082 0.643 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 679300 663.379 0.648 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 0 0 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 695536 679.234 0.663 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 518 628 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 713512 696.789 0.680 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 4 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 356 17 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 820541 801.310 0.783 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 828733 809.310 0.790 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 845117 825.310 0.806 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 877885 857.310 0.837 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 379 520 616 146 Total number of restraints before, now : 0 1661 make_re_422_> Number of previous, current restraints : 0 1661 make_re_423_> Number of previous, current selected restraints: 0 1661 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906708 885.457 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 make_re_422_> Number of previous, current restraints : 1661 1713 make_re_423_> Number of previous, current selected restraints: 1661 1713 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906808 885.555 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 omgdel__425_> Unselected all O C +N +CA dihedrals: 58 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 1713 1766 make_re_423_> Number of previous, current selected restraints: 1713 1708 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906808 885.555 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 make_re_422_> Number of previous, current restraints : 1766 1809 make_re_423_> Number of previous, current selected restraints: 1708 1751 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906808 885.555 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 make_re_422_> Number of previous, current restraints : 1809 1835 make_re_423_> Number of previous, current selected restraints: 1751 1777 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906808 885.555 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 make_re_422_> Number of previous, current restraints : 1835 1844 make_re_423_> Number of previous, current selected restraints: 1777 1786 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 906808 885.555 0.865 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 5fd1 getdata_643_> Protein accepted: 1fdn getdata_643_> Protein accepted: 1fxd getdata_643_> Protein accepted: 1iqz getdata_289_> Proteins (all/accepted): 4 4 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 939576 917.555 0.896 make_re_422_> Number of previous, current restraints : 1844 1845 make_re_423_> Number of previous, current selected restraints: 1786 1787 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1046964 1022.426 0.998 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1112500 1086.426 1.061 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1145268 1118.426 1.092 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1276340 1246.426 1.217 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1341876 1310.426 1.280 make_re_422_> Number of previous, current restraints : 1845 2632 make_re_423_> Number of previous, current selected restraints: 1787 2574 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1374644 1342.426 1.311 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1636788 1598.426 1.561 make_re_422_> Number of previous, current restraints : 2632 3529 make_re_423_> Number of previous, current selected restraints: 2574 3471 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1702324 1662.426 1.623 make_re_422_> Number of previous, current restraints : 3529 4229 make_re_423_> Number of previous, current selected restraints: 3471 4171 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2226612 2174.426 2.123 make_re_422_> Number of previous, current restraints : 4229 4426 make_re_423_> Number of previous, current selected restraints: 4171 4368 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4426 4426 make_re_423_> Number of previous, current selected restraints: 4368 4368 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4426 4426 make_re_423_> Number of previous, current selected restraints: 4368 4368 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4426 4426 make_re_423_> Number of previous, current selected restraints: 4368 4368 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4426 4426 make_re_423_> Number of previous, current selected restraints: 4368 4368 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 4426 4426 make_re_423_> Number of previous, current selected restraints: 4368 4368 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 4426 4054 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2076260 2027.598 1.980 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2174564 2123.598 2.074 rdcsr2__307_> Number of restraints read : 4054 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 4054 4054 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 2174584 2123.617 2.074 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 373 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 373 2332 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2585 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2757 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2938 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3366 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2476120 2418.086 2.361 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3669 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4033 pick_re_612_> Number of MODEL atoms, selected restraints; 373 4054 iupac_m_485_> OD1/2 will be swapped: -178.0612 31 31 iupac_m_485_> OD1/2 will be swapped: 118.8270 33 33 iupac_m_486_> OE1/2 will be swapped: 147.0036 53 53 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 373 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4054 4054 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 779 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 2327.1753 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 379 0 0 0.005 0.005 3.0873 1.000 2 Bond angle potential : 520 0 2 2.313 2.313 55.252 1.000 3 Stereochemical cosine torsion poten: 244 0 11 52.364 52.364 96.414 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.016 1.016 3.1725 1.000 5 Soft-sphere overlap restraints : 779 0 0 0.002 0.002 0.51144 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 787 0 2 1.067 1.067 655.85 1.000 10 Distance restraints 2 (N-O) : 897 0 6 1.109 1.109 768.22 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 53 0 3 5.750 5.750 20.663 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 78.326 78.326 11.118 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 44.543 44.543 9.0547 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 24.360 24.360 3.2554 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 90.393 90.393 1.1960 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 700 0 0 0.710 0.710 528.08 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 52 13 6 30.440 77.954 27.723 1.000 26 Distance restraints 4 (SDCH-SDCH) : 197 0 0 1.566 1.566 143.58 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open 1fdx.V99990001 # Heavy relative violation of each residue is written to: 1fdx.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 6423.2480 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1294 5N 6D C N 39 41 -85.48 -63.30 74.13 8.08 -63.30 74.13 8.08 1 6D 6D N CA 41 42 30.74 -40.00 -40.00 2 1296 7S 8C C N 53 55 -81.64 -69.10 44.96 3.27 -63.00 140.97 16.01 2 8C 8C N CA 55 56 98.63 141.80 -41.10 3 1297 8C 9I C N 59 61 -119.80 -120.60 1.68 0.07 -63.40 -178.58 28.07 3 9I 9I N CA 61 62 128.83 130.30 -43.60 4 1298 9I 10A C N 67 69 62.68 55.40 20.66 0.77 -62.50 138.71 28.19 4 10A 10A N CA 69 70 18.87 38.20 -40.90 5 1299 10A 11C C N 72 74 -132.02 -117.90 16.82 0.46 -63.00 -177.77 27.40 5 11C 11C N CA 74 75 150.24 141.10 -41.10 6 1300 11C 12G C N 78 80 176.31 -167.20 109.56 4.44 82.20 110.43 8.63 6 12G 12G N CA 80 81 66.28 174.60 8.50 7 1311 22I 23I C N 154 156 -63.68 -63.40 4.90 0.81 -120.60 -172.37 8.65 7 23I 23I N CA 156 157 -48.49 -43.60 130.30 8 1313 24Q 25G C N 171 173 157.65 -167.20 40.79 1.33 82.20 163.81 11.37 8 25G 25G N CA 173 174 153.91 174.60 8.50 9 1325 36I 37D C N 255 257 66.92 54.50 12.82 1.63 -63.30 154.99 26.41 9 37D 37D N CA 257 258 44.05 40.90 -40.00 10 1326 37D 38C C N 263 265 -92.83 -117.90 74.74 3.24 -63.00 111.46 15.81 10 38C 38C N CA 265 266 -148.49 141.10 -41.10 11 1327 38C 39G C N 269 271 -58.62 -62.40 6.63 1.19 82.20 147.62 11.16 11 39G 39G N CA 271 272 -35.75 -41.20 8.50 12 1329 40S 41C C N 279 281 -95.05 -63.00 73.27 11.34 -63.00 73.27 11.34 12 41C 41C N CA 281 282 -106.98 -41.10 -41.10 13 1341 52P 53E C N 354 356 -64.03 -69.30 11.91 0.72 -63.60 172.12 22.93 13 53E 53E N CA 356 357 131.82 142.50 -40.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 3 5 21 32 40 41 55 44 49 73 << end of ENERGY. openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990001.pdb 2327.17529 Dynamically allocated memory at finish [B,KiB,MiB]: 2476120 2418.086 2.361 Starting time : 2016/04/05 22:38:48 Closing time : 2016/04/05 22:38:51 Total CPU time [seconds] : 3.07