MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:27:12 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10693576 10442.945 10.198 read_mo_297_> Segments, residues, atoms: 14 7336 53970 read_mo_298_> Segment: 1 2 A 525 A 3855 read_mo_298_> Segment: 2 2 B 525 B 3855 read_mo_298_> Segment: 3 2 C 525 C 3855 read_mo_298_> Segment: 4 2 D 525 D 3855 read_mo_298_> Segment: 5 2 E 525 E 3855 read_mo_298_> Segment: 6 2 F 525 F 3855 read_mo_298_> Segment: 7 2 G 525 G 3855 read_mo_298_> Segment: 8 2 H 525 H 3855 read_mo_298_> Segment: 9 2 I 525 I 3855 read_mo_298_> Segment: 10 2 J 525 J 3855 read_mo_298_> Segment: 11 2 K 525 K 3855 read_mo_298_> Segment: 12 2 L 525 L 3855 read_mo_298_> Segment: 13 2 M 525 M 3855 read_mo_298_> Segment: 14 2 N 525 N 3855 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10906860 10651.230 10.402 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15038380 14685.918 14.342 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15104576 14750.562 14.405 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19236096 18785.250 18.345 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19290312 18838.195 18.397 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19450148 18994.285 18.549 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19609204 19149.613 18.701 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19663460 19202.598 18.753 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19823336 19358.727 18.905 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10487 12122 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994032 19525.422 19.068 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10489 12124 2897 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10489 12124 2897 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048288 19578.406 19.120 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10489 12124 4345 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208164 19734.535 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15732 18184 4345 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353220 19876.191 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15734 18186 4346 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15734 18186 4346 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407476 19929.176 19.462 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15734 18186 5794 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20567352 20085.305 19.615 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20977 24246 5794 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20776208 20289.266 19.814 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20979 24248 5795 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20979 24248 5795 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20830464 20342.250 19.865 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20979 24248 7243 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20990340 20498.379 20.018 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26222 30308 7243 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21127076 20631.910 20.148 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26224 30310 7244 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26224 30310 7244 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21181332 20684.895 20.200 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26224 30310 8692 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21341208 20841.023 20.353 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31467 36370 8692 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21505264 21001.234 20.509 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31469 36372 8693 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31469 36372 8693 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21570352 21064.797 20.571 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31469 36372 10141 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21730228 21220.926 20.724 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36712 42432 10141 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21927084 21413.168 20.911 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36714 42434 10142 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36714 42434 10142 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22005196 21489.449 20.986 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36714 42434 11590 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22165072 21645.578 21.138 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41957 48494 11590 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22401288 21876.258 21.364 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41959 48496 11591 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41959 48496 11591 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22495024 21967.797 21.453 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41959 48496 13039 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22654900 22123.926 21.605 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47202 54556 13039 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22938356 22400.738 21.876 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47204 54558 13040 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47204 54558 13040 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47204 54558 14488 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23098232 22556.867 22.028 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52447 60618 14488 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23098288 22556.922 22.028 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52449 60620 14489 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52449 60620 14489 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23210776 22666.773 22.136 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52449 60620 15937 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23370652 22822.902 22.288 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57692 66680 15937 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23710788 23155.066 22.612 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57694 66682 15938 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57694 66682 15938 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57694 66682 17386 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23870664 23311.195 22.765 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62937 72742 17386 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23870720 23311.250 22.765 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62939 72744 17387 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62939 72744 17387 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24005696 23443.062 22.894 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62939 72744 18835 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24165572 23599.191 23.046 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68182 78804 18835 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24573708 23997.762 23.435 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68184 78806 18836 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68184 78806 18836 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68184 78806 20284 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24733584 24153.891 23.588 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73427 84866 20284 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24733640 24153.945 23.588 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73429 84868 20285 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73429 84868 20285 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: 53968 16 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31185812 30454.895 29.741 read_mo_297_> Segments, residues, atoms: 14 7336 53970 read_mo_298_> Segment: 1 2 A 525 A 3855 read_mo_298_> Segment: 2 2 B 525 B 3855 read_mo_298_> Segment: 3 2 C 525 C 3855 read_mo_298_> Segment: 4 2 D 525 D 3855 read_mo_298_> Segment: 5 2 E 525 E 3855 read_mo_298_> Segment: 6 2 F 525 F 3855 read_mo_298_> Segment: 7 2 G 525 G 3855 read_mo_298_> Segment: 8 2 H 525 H 3855 read_mo_298_> Segment: 9 2 I 525 I 3855 read_mo_298_> Segment: 10 2 J 525 J 3855 read_mo_298_> Segment: 11 2 K 525 K 3855 read_mo_298_> Segment: 12 2 L 525 L 3855 read_mo_298_> Segment: 13 2 M 525 M 3855 read_mo_298_> Segment: 14 2 N 525 N 3855 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292280 30558.867 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31300472 30566.867 29.850 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31316856 30582.867 29.866 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31349624 30614.867 29.897 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31382392 30646.867 29.929 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31447928 30710.867 29.991 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31480696 30742.867 30.022 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31546232 30806.867 30.085 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31579000 30838.867 30.116 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31710072 30966.867 30.241 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31775608 31030.867 30.304 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31906680 31158.867 30.429 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31972216 31222.867 30.491 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32234360 31478.867 30.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32365432 31606.867 30.866 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32627576 31862.867 31.116 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32758648 31990.867 31.241 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33282936 32502.867 31.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33545080 32758.867 31.991 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34069368 33270.867 32.491 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34331512 33526.867 32.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35380088 34550.867 33.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35904376 35062.867 34.241 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36428664 35574.867 34.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37477240 36598.867 35.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39574392 38646.867 37.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40622968 39670.867 38.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41671544 40694.867 39.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43768696 42742.867 41.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47963000 46838.867 45.741 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50060152 48886.867 47.741 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73429 79492 20089 Total number of restraints before, now : 0 227386 make_re_422_> Number of previous, current restraints : 0 227386 make_re_423_> Number of previous, current selected restraints: 0 227386 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50060628 48887.332 47.742 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52157796 50935.348 49.742 make_re_422_> Number of previous, current restraints : 227386 234694 make_re_423_> Number of previous, current selected restraints: 227386 234694 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52157796 50935.348 49.742 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234694 242016 make_re_423_> Number of previous, current selected restraints: 234694 234498 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52157796 50935.348 49.742 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242016 247672 make_re_423_> Number of previous, current selected restraints: 234498 240154 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52157796 50935.348 49.742 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247672 251774 make_re_423_> Number of previous, current selected restraints: 240154 244256 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52157796 50935.348 49.742 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56352100 55031.348 53.742 make_re_422_> Number of previous, current restraints : 251774 253930 make_re_423_> Number of previous, current selected restraints: 244256 246412 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56352100 55031.348 53.742 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253930 254785 make_re_423_> Number of previous, current selected restraints: 246412 247267 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71899456 70214.312 68.569 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73337108 71618.266 69.940 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254785 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 60.3482 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 : 10 0 0 0.021 0.021 1.2357 1.000 2 Bond angle potential : 15 0 0 3.547 3.547 3.2680 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.254 36.254 5.7343 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.737 0.737 0.30279E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.465 0.465 47.905 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.342 0.342 0.27572E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.274 7.274 0.77510E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 2.614 2.614 -0.21946 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.42963E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.028 0.028 0.22263 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 30.356 36.073 2.0483 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 30 46 151 496 1472 3201 4236 4676 5782 7614 8906 9690 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254785 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 9.5381 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 : 10 0 0 0.006 0.006 0.10940 1.000 2 Bond angle potential : 15 0 0 3.330 3.330 2.8093 1.000 3 Stereochemical cosine torsion poten: 23 0 1 33.571 33.571 5.1835 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.620 0.620 0.36544E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 0 0.322 0.322 -1.0012 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.399 1.399 0.46176E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 9.352 9.352 0.13472 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.485 4.485 -0.14850 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 8.103 8.103 0.14547 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 11.057 11.057 0.29915 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.901 32.329 1.9236 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3200 4236 4676 5782 7614 8905 9691 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:33:02 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050584 19580.648 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210460 19736.777 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15731 18184 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355516 19878.434 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15733 18186 4345 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15733 18186 4345 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409772 19931.418 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15733 18186 5793 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569648 20087.547 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20976 24246 5793 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778504 20291.508 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20978 24248 5794 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20978 24248 5794 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832760 20344.492 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20978 24248 7242 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992636 20500.621 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26221 30308 7242 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129372 20634.152 20.151 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26223 30310 7243 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26223 30310 7243 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183628 20687.137 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26223 30310 8691 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343504 20843.266 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31466 36370 8691 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507560 21003.477 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31468 36372 8692 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31468 36372 8692 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572648 21067.039 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31468 36372 10140 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732524 21223.168 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36711 42432 10140 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929380 21415.410 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36713 42434 10141 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36713 42434 10141 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007492 21491.691 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36713 42434 11589 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167368 21647.820 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41956 48494 11589 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403584 21878.500 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41958 48496 11590 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41958 48496 11590 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497320 21970.039 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41958 48496 13038 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657196 22126.168 21.608 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47201 54556 13038 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940652 22402.980 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47203 54558 13039 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47203 54558 13039 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47203 54558 14487 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100528 22559.109 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52446 60618 14487 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100584 22559.164 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52448 60620 14488 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52448 60620 14488 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23213056 22669.000 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52448 60620 15936 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372932 22825.129 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57691 66680 15936 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23713068 23157.293 22.615 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57693 66682 15937 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57693 66682 15937 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57693 66682 17385 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872944 23313.422 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62936 72742 17385 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23873000 23313.477 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62938 72744 17386 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62938 72744 17386 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007976 23445.289 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62938 72744 18834 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167852 23601.418 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68181 78804 18834 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575988 23999.988 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68183 78806 18835 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68183 78806 18835 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68183 78806 20283 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735864 24156.117 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73426 84866 20283 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735920 24156.172 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73428 84868 20284 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73428 84868 20284 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189464 30458.461 29.745 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295932 30562.434 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31304124 30570.434 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320508 30586.434 29.870 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353276 30618.434 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31386044 30650.434 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451580 30714.434 29.995 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484348 30746.434 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549884 30810.434 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582652 30842.434 30.120 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713724 30970.434 30.245 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779260 31034.434 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910332 31162.434 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975868 31226.434 30.495 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32238012 31482.434 30.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32369084 31610.434 30.870 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631228 31866.434 31.120 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762300 31994.434 31.245 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286588 32506.434 31.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548732 32762.434 31.995 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34073020 33274.434 32.495 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34335164 33530.434 32.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383740 34554.434 33.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35908028 35066.434 34.245 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432316 35578.434 34.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480892 36602.434 35.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39578044 38650.434 37.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626620 39674.434 38.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41675196 40698.434 39.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772348 42746.434 41.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966652 46842.434 45.745 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063804 48890.434 47.745 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73428 79492 20088 Total number of restraints before, now : 0 227384 make_re_422_> Number of previous, current restraints : 0 227384 make_re_423_> Number of previous, current selected restraints: 0 227384 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063804 48890.434 47.745 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160972 50938.449 49.745 make_re_422_> Number of previous, current restraints : 227384 234692 make_re_423_> Number of previous, current selected restraints: 227384 234692 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160972 50938.449 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234692 242014 make_re_423_> Number of previous, current selected restraints: 234692 234496 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160972 50938.449 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242014 247670 make_re_423_> Number of previous, current selected restraints: 234496 240152 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160972 50938.449 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247670 251772 make_re_423_> Number of previous, current selected restraints: 240152 244254 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160972 50938.449 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355276 55034.449 53.745 make_re_422_> Number of previous, current restraints : 251772 253928 make_re_423_> Number of previous, current selected restraints: 244254 246410 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355276 55034.449 53.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253928 254784 make_re_423_> Number of previous, current selected restraints: 246410 247266 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902632 70217.414 68.572 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340284 71621.375 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254784 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 70.9662 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 : 10 0 0 0.022 0.022 1.2521 1.000 2 Bond angle potential : 15 0 0 3.501 3.501 3.2097 1.000 3 Stereochemical cosine torsion poten: 23 0 1 35.564 35.564 5.5284 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.809 0.809 0.33141E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.479 0.479 59.056 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.466 0.466 0.51174E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.479 7.479 0.82967E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 0.269 0.269 -0.23022 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.034 0.034 0.43192E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.044 0.044 0.22270 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 28.368 35.474 1.7632 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 724541881 2.282 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 9 29 46 151 496 1472 3200 4235 4675 5782 7613 8905 9693 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254784 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 9.5018 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 : 10 0 0 0.007 0.007 0.13362 1.000 2 Bond angle potential : 15 0 0 3.386 3.386 2.8934 1.000 3 Stereochemical cosine torsion poten: 23 0 1 33.570 33.570 5.1852 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.632 0.632 0.37264E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 0 0.320 0.320 -0.96544 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.848 0.848 0.16960E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 9.461 9.461 0.13856 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 5.593 5.593 -0.10709 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 8.249 8.249 0.14805 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 12.113 12.113 0.31212 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 25.444 32.105 1.7091 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3199 4235 4677 5779 7614 8904 9693 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:39:00 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409744 19931.391 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569620 20087.520 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20975 24246 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778476 20291.480 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20977 24248 5793 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20977 24248 5793 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832732 20344.465 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20977 24248 7241 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992608 20500.594 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26220 30308 7241 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129344 20634.125 20.151 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26222 30310 7242 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26222 30310 7242 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183600 20687.109 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26222 30310 8690 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343476 20843.238 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31465 36370 8690 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507532 21003.449 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31467 36372 8691 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31467 36372 8691 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572620 21067.012 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31467 36372 10139 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732496 21223.141 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36710 42432 10139 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929352 21415.383 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36712 42434 10140 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36712 42434 10140 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007448 21491.648 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36712 42434 11588 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167324 21647.777 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41955 48494 11588 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403540 21878.457 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41957 48496 11589 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41957 48496 11589 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497260 21969.980 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41957 48496 13037 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657136 22126.109 21.608 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47200 54556 13037 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940592 22402.922 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47202 54558 13038 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47202 54558 13038 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47202 54558 14486 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100468 22559.051 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52445 60618 14486 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100524 22559.105 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52447 60620 14487 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52447 60620 14487 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212996 22668.941 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52447 60620 15935 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372872 22825.070 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57690 66680 15935 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23713008 23157.234 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57692 66682 15936 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57692 66682 15936 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57692 66682 17384 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872884 23313.363 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62935 72742 17384 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872940 23313.418 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62937 72744 17385 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62937 72744 17385 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007900 23445.215 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62937 72744 18833 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167776 23601.344 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68180 78804 18833 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575912 23999.914 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68182 78806 18834 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68182 78806 18834 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68182 78806 20282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735788 24156.043 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73425 84866 20282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735844 24156.098 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73427 84868 20283 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73427 84868 20283 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189388 30458.387 29.745 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295856 30562.359 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31304048 30570.359 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320432 30586.359 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353200 30618.359 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385968 30650.359 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451504 30714.359 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484272 30746.359 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549808 30810.359 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582576 30842.359 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713648 30970.359 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779184 31034.359 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910256 31162.359 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975792 31226.359 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237936 31482.359 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32369008 31610.359 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631152 31866.359 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762224 31994.359 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286512 32506.359 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548656 32762.359 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072944 33274.359 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34335088 33530.359 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383664 34554.359 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907952 35066.359 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432240 35578.359 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480816 36602.359 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577968 38650.359 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626544 39674.359 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41675120 40698.359 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772272 42746.359 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966576 46842.359 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063728 48890.359 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73427 79492 20087 Total number of restraints before, now : 0 227382 make_re_422_> Number of previous, current restraints : 0 227382 make_re_423_> Number of previous, current selected restraints: 0 227382 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063728 48890.359 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160896 50938.375 49.745 make_re_422_> Number of previous, current restraints : 227382 234690 make_re_423_> Number of previous, current selected restraints: 227382 234690 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160896 50938.375 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234690 242012 make_re_423_> Number of previous, current selected restraints: 234690 234494 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160896 50938.375 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242012 247668 make_re_423_> Number of previous, current selected restraints: 234494 240150 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160896 50938.375 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247668 251770 make_re_423_> Number of previous, current selected restraints: 240150 244252 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160896 50938.375 49.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355200 55034.375 53.745 make_re_422_> Number of previous, current restraints : 251770 253926 make_re_423_> Number of previous, current selected restraints: 244252 246408 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355200 55034.375 53.745 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253926 254783 make_re_423_> Number of previous, current selected restraints: 246408 247265 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902556 70217.344 68.572 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340208 71621.297 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254783 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 117.3572 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 : 10 0 0 0.021 0.021 1.2173 1.000 2 Bond angle potential : 15 0 0 3.482 3.482 3.1483 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.341 36.341 5.6713 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.935 0.935 0.48370E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.510 0.510 105.22 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.420 0.420 0.41616E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.178 7.178 0.74984E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 0.811 0.811 -0.23040 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.42963E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.028 0.028 0.22263 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 30.594 35.368 1.9350 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1110138025 2.181 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 1 8 29 46 151 496 1472 3199 4235 4676 5778 7613 8906 9693 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254783 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 15.5626 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 : 10 0 0 0.009 0.009 0.20966 1.000 2 Bond angle potential : 15 0 0 4.092 4.092 4.4321 1.000 3 Stereochemical cosine torsion poten: 23 0 0 35.086 35.086 5.6920 1.000 4 Stereochemical improper torsion pot: 3 0 0 2.549 2.549 0.42619 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 0 0.388 0.388 -0.17011 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.441 1.441 0.49022E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 1 93.934 93.934 3.0017 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 14.792 14.792 0.18458 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 8.881 8.881 0.12892 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.052 0.052 0.21638 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 27.221 29.238 1.3921 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3198 4235 4676 5778 7613 8902 9697 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:44:50 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832704 20344.438 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992580 20500.566 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26219 30308 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129316 20634.098 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26221 30310 7241 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26221 30310 7241 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183572 20687.082 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26221 30310 8689 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343448 20843.211 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31464 36370 8689 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507504 21003.422 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31466 36372 8690 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31466 36372 8690 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572592 21066.984 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31466 36372 10138 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732468 21223.113 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36709 42432 10138 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929324 21415.355 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36711 42434 10139 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36711 42434 10139 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007420 21491.621 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36711 42434 11587 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167296 21647.750 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41954 48494 11587 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403512 21878.430 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41956 48496 11588 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41956 48496 11588 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497232 21969.953 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41956 48496 13036 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657108 22126.082 21.608 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47199 54556 13036 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940564 22402.895 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47201 54558 13037 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47201 54558 13037 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47201 54558 14485 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100440 22559.023 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52444 60618 14485 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100496 22559.078 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52446 60620 14486 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52446 60620 14486 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212968 22668.914 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52446 60620 15934 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372844 22825.043 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57689 66680 15934 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712980 23157.207 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57691 66682 15935 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57691 66682 15935 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57691 66682 17383 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872856 23313.336 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62934 72742 17383 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872912 23313.391 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62936 72744 17384 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62936 72744 17384 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007872 23445.188 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62936 72744 18832 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167748 23601.316 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68179 78804 18832 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575884 23999.887 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68181 78806 18833 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68181 78806 18833 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68181 78806 20281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735760 24156.016 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73424 84866 20281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735816 24156.070 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73426 84868 20282 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73426 84868 20282 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189360 30458.359 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295828 30562.332 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31304020 30570.332 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320404 30586.332 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353172 30618.332 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385940 30650.332 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451476 30714.332 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484244 30746.332 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549780 30810.332 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582548 30842.332 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713620 30970.332 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779156 31034.332 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910228 31162.332 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975764 31226.332 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237908 31482.332 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368980 31610.332 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631124 31866.332 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762196 31994.332 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286484 32506.332 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548628 32762.332 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072916 33274.332 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34335060 33530.332 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383636 34554.332 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907924 35066.332 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432212 35578.332 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480788 36602.332 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577940 38650.332 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626516 39674.332 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41675092 40698.332 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772244 42746.332 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966548 46842.332 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063700 48890.332 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73426 79492 20086 Total number of restraints before, now : 0 227380 make_re_422_> Number of previous, current restraints : 0 227380 make_re_423_> Number of previous, current selected restraints: 0 227380 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063700 48890.332 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160868 50938.348 49.744 make_re_422_> Number of previous, current restraints : 227380 234688 make_re_423_> Number of previous, current selected restraints: 227380 234688 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160868 50938.348 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234688 242010 make_re_423_> Number of previous, current selected restraints: 234688 234492 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160868 50938.348 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242010 247666 make_re_423_> Number of previous, current selected restraints: 234492 240148 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160868 50938.348 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247666 251768 make_re_423_> Number of previous, current selected restraints: 240148 244250 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160868 50938.348 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355172 55034.348 53.744 make_re_422_> Number of previous, current restraints : 251768 253924 make_re_423_> Number of previous, current selected restraints: 244250 246406 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355172 55034.348 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253924 254782 make_re_423_> Number of previous, current selected restraints: 246406 247264 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902528 70217.312 68.572 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340180 71621.266 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254782 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 198.2673 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 : 10 0 0 0.020 0.020 1.0292 1.000 2 Bond angle potential : 15 0 0 3.335 3.335 2.8677 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.259 36.259 5.6631 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.642 0.642 0.21864E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.519 0.519 186.53 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.290 0.290 0.19907E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 6.353 6.353 0.54661E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 2.003 2.003 -0.22506 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.034 0.034 0.21619 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 30.685 35.886 2.0781 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1495734169 2.083 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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: 1 0 8 29 46 151 496 1472 3198 4234 4676 5779 7613 8901 9697 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254782 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 27 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 14.8493 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 : 10 0 0 0.009 0.009 0.24568 1.000 2 Bond angle potential : 15 0 0 3.873 3.873 3.9620 1.000 3 Stereochemical cosine torsion poten: 23 0 0 34.867 34.867 5.6453 1.000 4 Stereochemical improper torsion pot: 3 0 0 2.135 2.135 0.30648 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 27 0 0 0.376 0.376 -0.41548 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.649 0.649 0.99346E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 1 94.027 94.027 2.9905 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 14.576 14.576 0.16325 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 2.522 2.522 0.60756E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 27.146 30.895 1.6651 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3197 4234 4676 5778 7612 8900 9699 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:50:39 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183544 20687.055 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343420 20843.184 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31463 36370 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507476 21003.395 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31465 36372 8689 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31465 36372 8689 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572548 21066.941 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31465 36372 10137 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732424 21223.070 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36708 42432 10137 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929280 21415.312 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36710 42434 10138 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36710 42434 10138 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007376 21491.578 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36710 42434 11586 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167252 21647.707 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41953 48494 11586 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403468 21878.387 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41955 48496 11587 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41955 48496 11587 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497188 21969.910 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41955 48496 13035 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657064 22126.039 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47198 54556 13035 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940520 22402.852 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47200 54558 13036 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47200 54558 13036 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47200 54558 14484 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100396 22558.980 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52443 60618 14484 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100452 22559.035 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52445 60620 14485 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52445 60620 14485 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212908 22668.855 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52445 60620 15933 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372784 22824.984 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57688 66680 15933 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712920 23157.148 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57690 66682 15934 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57690 66682 15934 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57690 66682 17382 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872796 23313.277 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62933 72742 17382 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872852 23313.332 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62935 72744 17383 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62935 72744 17383 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007812 23445.129 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62935 72744 18831 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167688 23601.258 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68178 78804 18831 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575824 23999.828 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68180 78806 18832 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68180 78806 18832 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68180 78806 20280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735700 24155.957 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73423 84866 20280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735756 24156.012 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73425 84868 20281 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73425 84868 20281 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189300 30458.301 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295768 30562.273 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303960 30570.273 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320344 30586.273 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353112 30618.273 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385880 30650.273 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451416 30714.273 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484184 30746.273 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549720 30810.273 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582488 30842.273 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713560 30970.273 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779096 31034.273 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910168 31162.273 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975704 31226.273 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237848 31482.273 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368920 31610.273 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631064 31866.273 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762136 31994.273 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286424 32506.273 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548568 32762.273 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072856 33274.273 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34335000 33530.273 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383576 34554.273 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907864 35066.273 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432152 35578.273 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480728 36602.273 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577880 38650.273 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626456 39674.273 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41675032 40698.273 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772184 42746.273 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966488 46842.273 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063640 48890.273 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73425 79492 20085 Total number of restraints before, now : 0 227378 make_re_422_> Number of previous, current restraints : 0 227378 make_re_423_> Number of previous, current selected restraints: 0 227378 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063640 48890.273 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160808 50938.289 49.744 make_re_422_> Number of previous, current restraints : 227378 234686 make_re_423_> Number of previous, current selected restraints: 227378 234686 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160808 50938.289 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234686 242008 make_re_423_> Number of previous, current selected restraints: 234686 234490 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160808 50938.289 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242008 247664 make_re_423_> Number of previous, current selected restraints: 234490 240146 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160808 50938.289 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247664 251766 make_re_423_> Number of previous, current selected restraints: 240146 244248 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160808 50938.289 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355112 55034.289 53.744 make_re_422_> Number of previous, current restraints : 251766 253922 make_re_423_> Number of previous, current selected restraints: 244248 246404 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355112 55034.289 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253922 254781 make_re_423_> Number of previous, current selected restraints: 246404 247263 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902468 70217.250 68.572 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340120 71621.211 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254781 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 21.1483 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 : 10 0 0 0.021 0.021 1.2635 1.000 2 Bond angle potential : 15 0 0 3.498 3.498 3.1866 1.000 3 Stereochemical cosine torsion poten: 23 0 1 35.872 35.872 5.5887 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.899 0.899 0.41168E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 1 0.415 0.415 9.0241 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.439 0.439 0.45450E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 5.842 5.842 0.43220E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 1.010 1.010 -0.23005 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.34081E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.040 0.040 0.22268 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 29.983 35.594 1.9698 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 497 1472 3197 4234 4676 5777 7611 8900 9698 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254781 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 9.5601 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 : 10 0 0 0.006 0.006 0.10757 1.000 2 Bond angle potential : 15 0 0 3.361 3.361 2.8949 1.000 3 Stereochemical cosine torsion poten: 23 0 1 33.398 33.398 5.1807 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.666 0.666 0.48618E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 0 0.324 0.324 -0.90351 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.962 0.962 0.21856E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.559 7.559 0.77948E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.047 4.047 -0.16249 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 7.318 7.318 0.13213 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 12.131 12.131 0.31236 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.471 31.559 1.8501 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3196 4234 4676 5777 7610 8899 9701 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/11/30 23:56:29 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732396 21223.043 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36707 42432 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929252 21415.285 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36709 42434 10137 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36709 42434 10137 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007348 21491.551 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36709 42434 11585 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167224 21647.680 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41952 48494 11585 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403440 21878.359 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41954 48496 11586 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41954 48496 11586 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497160 21969.883 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41954 48496 13034 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657036 22126.012 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47197 54556 13034 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940492 22402.824 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47199 54558 13035 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47199 54558 13035 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47199 54558 14483 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100368 22558.953 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52442 60618 14483 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100424 22559.008 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52444 60620 14484 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52444 60620 14484 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212880 22668.828 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52444 60620 15932 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372756 22824.957 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57687 66680 15932 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712892 23157.121 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57689 66682 15933 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57689 66682 15933 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57689 66682 17381 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872768 23313.250 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62932 72742 17381 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872824 23313.305 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62934 72744 17382 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62934 72744 17382 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007768 23445.086 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62934 72744 18830 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167644 23601.215 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68177 78804 18830 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575780 23999.785 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68179 78806 18831 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68179 78806 18831 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68179 78806 20279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735656 24155.914 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73422 84866 20279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735712 24155.969 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73424 84868 20280 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73424 84868 20280 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189256 30458.258 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295724 30562.230 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303916 30570.230 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320300 30586.230 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353068 30618.230 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385836 30650.230 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451372 30714.230 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484140 30746.230 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549676 30810.230 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582444 30842.230 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713516 30970.230 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779052 31034.230 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910124 31162.230 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975660 31226.230 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237804 31482.230 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368876 31610.230 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631020 31866.230 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762092 31994.230 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286380 32506.230 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548524 32762.230 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072812 33274.230 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334956 33530.230 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383532 34554.230 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907820 35066.230 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432108 35578.230 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480684 36602.230 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577836 38650.230 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626412 39674.230 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674988 40698.230 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772140 42746.230 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966444 46842.230 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063596 48890.230 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73424 79492 20084 Total number of restraints before, now : 0 227376 make_re_422_> Number of previous, current restraints : 0 227376 make_re_423_> Number of previous, current selected restraints: 0 227376 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063596 48890.230 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160764 50938.246 49.744 make_re_422_> Number of previous, current restraints : 227376 234684 make_re_423_> Number of previous, current selected restraints: 227376 234684 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160764 50938.246 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234684 242006 make_re_423_> Number of previous, current selected restraints: 234684 234488 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160764 50938.246 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242006 247662 make_re_423_> Number of previous, current selected restraints: 234488 240144 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160764 50938.246 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247662 251764 make_re_423_> Number of previous, current selected restraints: 240144 244246 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160764 50938.246 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355068 55034.246 53.744 make_re_422_> Number of previous, current restraints : 251764 253920 make_re_423_> Number of previous, current selected restraints: 244246 246402 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355068 55034.246 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253920 254780 make_re_423_> Number of previous, current selected restraints: 246402 247262 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902424 70217.211 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340076 71621.172 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254780 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 51.0689 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 : 10 0 0 0.023 0.023 1.3866 1.000 2 Bond angle potential : 15 0 0 3.584 3.584 3.3764 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.646 36.646 5.8328 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.901 0.901 0.43474E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.480 0.480 37.638 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.707 0.707 0.11787E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.780 7.780 0.91248E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 1.132 1.132 -0.22972 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.028 0.028 0.21613 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 31.565 41.509 2.6681 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 30 46 151 496 1472 3194 4234 4676 5777 7610 8899 9701 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254780 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 10.1461 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 : 10 0 0 0.007 0.007 0.11580 1.000 2 Bond angle potential : 15 0 0 3.383 3.383 2.8717 1.000 3 Stereochemical cosine torsion poten: 23 0 1 33.820 33.820 5.2376 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.573 0.573 0.31030E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 0 0.328 0.328 -0.96265 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.386 1.386 0.45346E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 8.087 8.087 0.93347E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 5.094 5.094 -0.12681 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 6.946 6.946 0.12608 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 9.393 9.393 0.28141 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 27.979 37.788 2.4332 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3193 4234 4676 5777 7608 8900 9701 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:02:19 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167212 21647.668 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41951 48494 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403428 21878.348 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41953 48496 11585 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41953 48496 11585 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497148 21969.871 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41953 48496 13033 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657024 22126.000 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47196 54556 13033 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940480 22402.812 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47198 54558 13034 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47198 54558 13034 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47198 54558 14482 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100356 22558.941 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52441 60618 14482 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100412 22558.996 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52443 60620 14483 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52443 60620 14483 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212868 22668.816 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52443 60620 15931 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372744 22824.945 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57686 66680 15931 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712880 23157.109 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57688 66682 15932 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57688 66682 15932 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57688 66682 17380 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872756 23313.238 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62931 72742 17380 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872812 23313.293 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62933 72744 17381 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62933 72744 17381 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007756 23445.074 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62933 72744 18829 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167632 23601.203 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68176 78804 18829 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575768 23999.773 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68178 78806 18830 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68178 78806 18830 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68178 78806 20278 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735644 24155.902 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73421 84866 20278 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735700 24155.957 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73423 84868 20279 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73423 84868 20279 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189244 30458.246 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295712 30562.219 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303904 30570.219 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320288 30586.219 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353056 30618.219 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385824 30650.219 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451360 30714.219 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484128 30746.219 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549664 30810.219 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582432 30842.219 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713504 30970.219 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779040 31034.219 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910112 31162.219 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975648 31226.219 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237792 31482.219 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368864 31610.219 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32631008 31866.219 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762080 31994.219 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286368 32506.219 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548512 32762.219 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072800 33274.219 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334944 33530.219 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383520 34554.219 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907808 35066.219 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432096 35578.219 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480672 36602.219 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577824 38650.219 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626400 39674.219 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674976 40698.219 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772128 42746.219 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966432 46842.219 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063584 48890.219 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73423 79492 20083 Total number of restraints before, now : 0 227374 make_re_422_> Number of previous, current restraints : 0 227374 make_re_423_> Number of previous, current selected restraints: 0 227374 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063584 48890.219 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160752 50938.234 49.744 make_re_422_> Number of previous, current restraints : 227374 234682 make_re_423_> Number of previous, current selected restraints: 227374 234682 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160752 50938.234 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234682 242004 make_re_423_> Number of previous, current selected restraints: 234682 234486 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160752 50938.234 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242004 247660 make_re_423_> Number of previous, current selected restraints: 234486 240142 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160752 50938.234 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247660 251762 make_re_423_> Number of previous, current selected restraints: 240142 244244 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160752 50938.234 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355056 55034.234 53.744 make_re_422_> Number of previous, current restraints : 251762 253918 make_re_423_> Number of previous, current selected restraints: 244244 246400 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355056 55034.234 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253918 254779 make_re_423_> Number of previous, current selected restraints: 246400 247261 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902412 70217.203 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340064 71621.156 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254779 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 67.2226 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 : 10 0 0 0.021 0.021 1.2234 1.000 2 Bond angle potential : 15 0 0 3.423 3.423 3.0569 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.782 36.782 5.8395 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.794 0.794 0.32133E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.487 0.487 54.909 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.158 0.158 0.58662E-03 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 8.184 8.184 0.10283 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 1.155 1.155 -0.22965 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 30.910 36.298 2.0375 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2652549593 2.297 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 9 29 46 151 496 1472 3193 4234 4675 5776 7608 8899 9703 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254779 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 10.3925 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 : 10 0 0 0.006 0.006 0.10639 1.000 2 Bond angle potential : 15 0 0 3.680 3.680 3.6005 1.000 3 Stereochemical cosine torsion poten: 23 0 0 33.863 33.863 5.3156 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.154 1.154 0.10280 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 0 0.316 0.316 -0.75476 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.601 0.601 0.85170E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 1.552 1.552 -0.20094E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 6.596 6.596 -0.62132E-01 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 6.371 6.371 0.11706 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 17.910 17.910 0.41296 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.771 30.425 1.5657 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3192 4234 4675 5776 7608 8898 9702 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:08:09 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13032 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657012 22125.988 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47195 54556 13032 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940468 22402.801 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47197 54558 13033 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47197 54558 13033 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47197 54558 14481 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100344 22558.930 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52440 60618 14481 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100400 22558.984 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52442 60620 14482 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52442 60620 14482 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212856 22668.805 22.138 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52442 60620 15930 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372732 22824.934 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57685 66680 15930 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712868 23157.098 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57687 66682 15931 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57687 66682 15931 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57687 66682 17379 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872744 23313.227 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62930 72742 17379 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872800 23313.281 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62932 72744 17380 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62932 72744 17380 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007744 23445.062 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62932 72744 18828 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167620 23601.191 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68175 78804 18828 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575756 23999.762 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68177 78806 18829 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68177 78806 18829 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68177 78806 20277 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735632 24155.891 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73420 84866 20277 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735688 24155.945 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73422 84868 20278 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73422 84868 20278 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189232 30458.234 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295700 30562.207 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303892 30570.207 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320276 30586.207 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353044 30618.207 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385812 30650.207 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451348 30714.207 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484116 30746.207 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549652 30810.207 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582420 30842.207 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713492 30970.207 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779028 31034.207 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910100 31162.207 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975636 31226.207 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237780 31482.207 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368852 31610.207 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630996 31866.207 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762068 31994.207 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286356 32506.207 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548500 32762.207 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072788 33274.207 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334932 33530.207 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383508 34554.207 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907796 35066.207 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432084 35578.207 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480660 36602.207 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577812 38650.207 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626388 39674.207 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674964 40698.207 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772116 42746.207 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966420 46842.207 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063572 48890.207 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73422 79492 20082 Total number of restraints before, now : 0 227372 make_re_422_> Number of previous, current restraints : 0 227372 make_re_423_> Number of previous, current selected restraints: 0 227372 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063572 48890.207 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160740 50938.223 49.744 make_re_422_> Number of previous, current restraints : 227372 234680 make_re_423_> Number of previous, current selected restraints: 227372 234680 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160740 50938.223 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234680 242002 make_re_423_> Number of previous, current selected restraints: 234680 234484 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160740 50938.223 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242002 247658 make_re_423_> Number of previous, current selected restraints: 234484 240140 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160740 50938.223 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247658 251760 make_re_423_> Number of previous, current selected restraints: 240140 244242 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160740 50938.223 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355044 55034.223 53.744 make_re_422_> Number of previous, current restraints : 251760 253916 make_re_423_> Number of previous, current selected restraints: 244242 246398 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355044 55034.223 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253916 254778 make_re_423_> Number of previous, current selected restraints: 246398 247260 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902400 70217.188 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340052 71621.141 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254778 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 35.2886 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 : 10 0 0 0.022 0.022 1.3535 1.000 2 Bond angle potential : 15 0 0 3.510 3.510 3.3642 1.000 3 Stereochemical cosine torsion poten: 23 0 1 37.493 37.493 6.0030 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.911 0.911 0.46292E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 1 0.464 0.464 22.272 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.336 0.336 0.26651E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.648 7.648 0.87568E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.118 4.118 -0.19807 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.34081E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.040 0.040 0.22268 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 32.912 36.235 2.1003 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 47 151 496 1472 3192 4233 4675 5776 7608 8898 9702 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254778 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 26 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 11.9526 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 : 10 0 0 0.004 0.004 0.44820E-01 1.000 2 Bond angle potential : 15 0 0 3.412 3.412 3.1211 1.000 3 Stereochemical cosine torsion poten: 23 0 0 33.921 33.921 5.3887 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.964 0.964 0.65520E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 26 0 0 0.353 0.353 -0.67824 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.897 0.897 0.18992E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 91.894 91.894 0.74421 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 96.602 96.602 0.78737 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 105.426 105.426 1.0969 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 27.874 28.987 1.3288 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3191 4233 4675 5774 7608 8898 9704 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:14:03 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100332 22558.918 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52439 60618 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100388 22558.973 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52441 60620 14481 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52441 60620 14481 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212844 22668.793 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52441 60620 15929 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372720 22824.922 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57684 66680 15929 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712856 23157.086 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57686 66682 15930 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57686 66682 15930 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57686 66682 17378 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872732 23313.215 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62929 72742 17378 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872788 23313.270 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62931 72744 17379 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62931 72744 17379 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007732 23445.051 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62931 72744 18827 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167608 23601.180 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68174 78804 18827 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575744 23999.750 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68176 78806 18828 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68176 78806 18828 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68176 78806 20276 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735620 24155.879 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73419 84866 20276 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735676 24155.934 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73421 84868 20277 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73421 84868 20277 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189220 30458.223 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295688 30562.195 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303880 30570.195 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320264 30586.195 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353032 30618.195 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385800 30650.195 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451336 30714.195 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484104 30746.195 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549640 30810.195 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582408 30842.195 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713480 30970.195 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779016 31034.195 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910088 31162.195 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975624 31226.195 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237768 31482.195 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368840 31610.195 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630984 31866.195 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762056 31994.195 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286344 32506.195 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548488 32762.195 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072776 33274.195 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334920 33530.195 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383496 34554.195 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907784 35066.195 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432072 35578.195 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480648 36602.195 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577800 38650.195 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626376 39674.195 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674952 40698.195 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772104 42746.195 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966408 46842.195 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063560 48890.195 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73421 79492 20081 Total number of restraints before, now : 0 227370 make_re_422_> Number of previous, current restraints : 0 227370 make_re_423_> Number of previous, current selected restraints: 0 227370 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063560 48890.195 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160728 50938.211 49.744 make_re_422_> Number of previous, current restraints : 227370 234678 make_re_423_> Number of previous, current selected restraints: 227370 234678 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160728 50938.211 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234678 242000 make_re_423_> Number of previous, current selected restraints: 234678 234482 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160728 50938.211 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 242000 247656 make_re_423_> Number of previous, current selected restraints: 234482 240138 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160728 50938.211 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247656 251758 make_re_423_> Number of previous, current selected restraints: 240138 244240 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160728 50938.211 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355032 55034.211 53.744 make_re_422_> Number of previous, current restraints : 251758 253914 make_re_423_> Number of previous, current selected restraints: 244240 246396 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355032 55034.211 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253914 254777 make_re_423_> Number of previous, current selected restraints: 246396 247259 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902388 70217.172 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340040 71621.133 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254777 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 163.5932 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 : 10 0 0 0.021 0.021 1.2136 1.000 2 Bond angle potential : 15 0 0 3.512 3.512 3.2813 1.000 3 Stereochemical cosine torsion poten: 23 0 1 37.074 37.074 5.8544 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.882 0.882 0.41688E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.518 0.518 150.85 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.132 0.132 0.41111E-03 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 9.426 9.426 0.14180 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.818 4.818 -0.18471 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.34081E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 32.883 36.200 2.1405 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1488934237 2.119 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 1 8 29 46 151 496 1472 3191 4232 4675 5773 7609 8899 9704 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254777 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 20 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.6401 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 : 10 0 0 0.006 0.006 0.10230 1.000 2 Bond angle potential : 15 0 0 3.292 3.292 2.7996 1.000 3 Stereochemical cosine torsion poten: 23 0 0 40.853 40.853 5.4926 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.678 0.678 0.34286E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 20 0 0 0.348 0.348 -0.14635E-01 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.677 1.677 0.66393E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 5.406 5.406 0.34169E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 94.469 94.469 0.82187 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 110.826 110.826 1.2709 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 29.008 31.241 1.8167 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3190 4232 4676 5772 7608 8896 9706 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:19:52 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15928 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372708 22824.910 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57683 66680 15928 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712844 23157.074 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57685 66682 15929 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57685 66682 15929 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57685 66682 17377 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872720 23313.203 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62928 72742 17377 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872776 23313.258 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62930 72744 17378 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62930 72744 17378 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007720 23445.039 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62930 72744 18826 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167596 23601.168 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68173 78804 18826 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575732 23999.738 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68175 78806 18827 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68175 78806 18827 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68175 78806 20275 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735608 24155.867 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73418 84866 20275 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735664 24155.922 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73420 84868 20276 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73420 84868 20276 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189208 30458.211 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295676 30562.184 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303868 30570.184 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320252 30586.184 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353020 30618.184 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385788 30650.184 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451324 30714.184 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484092 30746.184 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549628 30810.184 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582396 30842.184 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713468 30970.184 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779004 31034.184 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910076 31162.184 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975612 31226.184 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237756 31482.184 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368828 31610.184 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630972 31866.184 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762044 31994.184 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286332 32506.184 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548476 32762.184 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072764 33274.184 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334908 33530.184 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383484 34554.184 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907772 35066.184 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432060 35578.184 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480636 36602.184 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577788 38650.184 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626364 39674.184 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674940 40698.184 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772092 42746.184 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966396 46842.184 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063548 48890.184 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73420 79492 20080 Total number of restraints before, now : 0 227368 make_re_422_> Number of previous, current restraints : 0 227368 make_re_423_> Number of previous, current selected restraints: 0 227368 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063548 48890.184 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160716 50938.199 49.744 make_re_422_> Number of previous, current restraints : 227368 234676 make_re_423_> Number of previous, current selected restraints: 227368 234676 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234676 241998 make_re_423_> Number of previous, current selected restraints: 234676 234480 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241998 247654 make_re_423_> Number of previous, current selected restraints: 234480 240136 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247654 251756 make_re_423_> Number of previous, current selected restraints: 240136 244238 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355020 55034.199 53.744 make_re_422_> Number of previous, current restraints : 251756 253912 make_re_423_> Number of previous, current selected restraints: 244238 246394 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355020 55034.199 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253912 254776 make_re_423_> Number of previous, current selected restraints: 246394 247258 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902376 70217.164 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340028 71621.125 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254776 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 104.3265 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 : 10 0 0 0.023 0.023 1.4008 1.000 2 Bond angle potential : 15 0 0 3.572 3.572 3.4513 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.843 36.843 5.7997 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.038 1.038 0.55163E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 1 0.490 0.490 91.682 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.411 0.411 0.39862E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 6.501 6.501 0.58131E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 3.939 3.939 -0.20114 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.040 0.040 0.21625 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 32.175 35.207 1.8264 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1103338093 2.205 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 9 29 46 151 496 1472 3190 4231 4676 5772 7607 8898 9706 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254776 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 21 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.8566 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 : 10 0 0 0.007 0.007 0.11268 1.000 2 Bond angle potential : 15 0 0 3.339 3.339 2.8888 1.000 3 Stereochemical cosine torsion poten: 23 0 0 40.600 40.600 5.4219 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.547 0.547 0.21757E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 21 0 0 0.340 0.340 -0.43286 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.422 1.422 0.47724E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 3.195 3.195 -0.17333E-02 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 90.296 90.296 0.95300 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 109.646 109.646 1.2687 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 113.522 113.522 1.1088 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 28.259 30.203 1.4679 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3189 4231 4677 5770 7607 8896 9706 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:25:42 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from LYS to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15928 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372708 22824.910 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57683 66680 15928 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712844 23157.074 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57685 66682 15929 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57685 66682 15929 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57685 66682 17377 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872720 23313.203 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62928 72742 17377 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872776 23313.258 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62930 72744 17378 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62930 72744 17378 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007720 23445.039 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62930 72744 18826 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167596 23601.168 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68173 78804 18826 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575732 23999.738 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68175 78806 18827 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68175 78806 18827 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68175 78806 20275 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735608 24155.867 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73418 84866 20275 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735664 24155.922 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73420 84868 20276 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73420 84868 20276 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: 53984 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189208 30458.211 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295676 30562.184 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303868 30570.184 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320252 30586.184 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353020 30618.184 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385788 30650.184 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451324 30714.184 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484092 30746.184 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549628 30810.184 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582396 30842.184 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713468 30970.184 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31779004 31034.184 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910076 31162.184 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975612 31226.184 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237756 31482.184 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368828 31610.184 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630972 31866.184 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762044 31994.184 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286332 32506.184 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548476 32762.184 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072764 33274.184 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334908 33530.184 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383484 34554.184 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907772 35066.184 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432060 35578.184 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480636 36602.184 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577788 38650.184 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626364 39674.184 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674940 40698.184 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772092 42746.184 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966396 46842.184 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063548 48890.184 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73420 79492 20080 Total number of restraints before, now : 0 227368 make_re_422_> Number of previous, current restraints : 0 227368 make_re_423_> Number of previous, current selected restraints: 0 227368 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063548 48890.184 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160716 50938.199 49.744 make_re_422_> Number of previous, current restraints : 227368 234676 make_re_423_> Number of previous, current selected restraints: 227368 234676 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234676 241998 make_re_423_> Number of previous, current selected restraints: 234676 234480 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241998 247654 make_re_423_> Number of previous, current selected restraints: 234480 240136 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247654 251756 make_re_423_> Number of previous, current selected restraints: 240136 244238 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160716 50938.199 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355020 55034.199 53.744 make_re_422_> Number of previous, current restraints : 251756 253912 make_re_423_> Number of previous, current selected restraints: 244238 246394 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355020 55034.199 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253912 254776 make_re_423_> Number of previous, current selected restraints: 246394 247258 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902376 70217.164 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340028 71621.125 69.943 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254776 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 20 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.2469 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 : 10 0 0 0.006 0.006 0.10575 1.000 2 Bond angle potential : 15 0 0 3.294 3.294 2.8011 1.000 3 Stereochemical cosine torsion poten: 23 0 0 40.855 40.855 5.4922 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.671 0.671 0.33817E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 20 0 0 0.348 0.348 -0.17619E-01 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.673 1.673 0.66065E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 5.395 5.395 -0.40378E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 94.485 94.485 0.72433 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 110.819 110.819 1.0489 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.028 0.028 0.21613 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 29.025 31.232 1.8167 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3189 4231 4677 5770 7607 8896 9706 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254776 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.7364 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 : 10 0 0 0.006 0.006 0.94283E-01 1.000 2 Bond angle potential : 15 0 0 3.393 3.393 3.0220 1.000 3 Stereochemical cosine torsion poten: 23 0 0 36.786 36.786 5.3898 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.667 0.667 0.32498E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 0 0.374 0.374 -0.15566 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.661 1.661 0.65145E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 6.822 6.822 -0.82946E-02 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 92.424 92.424 0.77883 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 72.022 72.022 1.5283 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.22251 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 28.640 30.887 1.7670 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3189 4231 4677 5770 7606 8897 9706 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:31:33 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372696 22824.898 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57682 66680 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712832 23157.062 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57684 66682 17376 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872708 23313.191 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62927 72742 17376 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872764 23313.246 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62929 72744 17377 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62929 72744 17377 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007708 23445.027 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62929 72744 18825 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167584 23601.156 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68172 78804 18825 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575720 23999.727 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68174 78806 18826 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68174 78806 18826 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68174 78806 20274 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735596 24155.855 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73417 84866 20274 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735652 24155.910 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73419 84868 20275 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73419 84868 20275 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189196 30458.199 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295664 30562.172 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303856 30570.172 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320240 30586.172 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31353008 30618.172 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385776 30650.172 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451312 30714.172 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484080 30746.172 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549616 30810.172 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582384 30842.172 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713456 30970.172 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31778992 31034.172 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910064 31162.172 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975600 31226.172 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237744 31482.172 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368816 31610.172 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630960 31866.172 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762032 31994.172 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286320 32506.172 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548464 32762.172 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072752 33274.172 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334896 33530.172 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383472 34554.172 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907760 35066.172 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432048 35578.172 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480624 36602.172 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577776 38650.172 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626352 39674.172 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674928 40698.172 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772080 42746.172 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966384 46842.172 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063536 48890.172 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73419 79492 20079 Total number of restraints before, now : 0 227366 make_re_422_> Number of previous, current restraints : 0 227366 make_re_423_> Number of previous, current selected restraints: 0 227366 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063536 48890.172 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160704 50938.188 49.744 make_re_422_> Number of previous, current restraints : 227366 234674 make_re_423_> Number of previous, current selected restraints: 227366 234674 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160704 50938.188 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234674 241996 make_re_423_> Number of previous, current selected restraints: 234674 234478 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160704 50938.188 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241996 247652 make_re_423_> Number of previous, current selected restraints: 234478 240134 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160704 50938.188 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247652 251754 make_re_423_> Number of previous, current selected restraints: 240134 244236 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160704 50938.188 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56355008 55034.188 53.744 make_re_422_> Number of previous, current restraints : 251754 253910 make_re_423_> Number of previous, current selected restraints: 244236 246392 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56355008 55034.188 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253910 254775 make_re_423_> Number of previous, current selected restraints: 246392 247257 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902364 70217.156 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340016 71621.109 69.942 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254775 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 24 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 37.6675 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 : 10 0 0 0.022 0.022 1.3411 1.000 2 Bond angle potential : 15 0 0 3.527 3.527 3.3814 1.000 3 Stereochemical cosine torsion poten: 23 0 1 37.150 37.150 5.9333 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.018 1.018 0.57858E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 24 0 1 0.460 0.460 24.819 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.348 0.348 0.28590E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.760 7.760 0.90695E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.096 4.096 -0.19845 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 32.105 35.823 1.9892 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 47 151 496 1472 3189 4230 4677 5770 7606 8897 9706 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254775 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.1302 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 : 10 0 0 0.004 0.004 0.49153E-01 1.000 2 Bond angle potential : 15 0 0 3.400 3.400 3.1204 1.000 3 Stereochemical cosine torsion poten: 23 0 0 37.945 37.945 5.3459 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.108 1.108 0.91123E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 0 0.312 0.312 -0.88663 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.912 0.912 0.19639E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 0.506 0.506 -0.22175E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 135.620 135.620 0.57494 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 87.787 87.787 1.3443 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 95.562 95.562 1.1431 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.953 29.043 1.3505 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3188 4230 4677 5770 7604 8897 9708 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:37:22 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372696 22824.898 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57682 66680 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712832 23157.062 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57684 66682 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872696 23313.180 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62926 72742 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872752 23313.234 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007696 23445.016 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62928 72744 18824 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167572 23601.145 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68171 78804 18824 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575708 23999.715 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68173 78806 18825 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68173 78806 18825 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68173 78806 20273 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735584 24155.844 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73416 84866 20273 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735640 24155.898 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73418 84868 20274 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73418 84868 20274 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189184 30458.188 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295652 30562.160 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303844 30570.160 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320228 30586.160 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31352996 30618.160 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385764 30650.160 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451300 30714.160 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484068 30746.160 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549604 30810.160 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582372 30842.160 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713444 30970.160 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31778980 31034.160 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910052 31162.160 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975588 31226.160 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237732 31482.160 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368804 31610.160 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630948 31866.160 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762020 31994.160 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286308 32506.160 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548452 32762.160 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072740 33274.160 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334884 33530.160 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383460 34554.160 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907748 35066.160 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432036 35578.160 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480612 36602.160 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577764 38650.160 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626340 39674.160 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674916 40698.160 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772068 42746.160 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966372 46842.160 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063524 48890.160 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73418 79492 20078 Total number of restraints before, now : 0 227364 make_re_422_> Number of previous, current restraints : 0 227364 make_re_423_> Number of previous, current selected restraints: 0 227364 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063524 48890.160 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160692 50938.176 49.744 make_re_422_> Number of previous, current restraints : 227364 234672 make_re_423_> Number of previous, current selected restraints: 227364 234672 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160692 50938.176 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234672 241994 make_re_423_> Number of previous, current selected restraints: 234672 234476 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160692 50938.176 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241994 247650 make_re_423_> Number of previous, current selected restraints: 234476 240132 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160692 50938.176 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247650 251752 make_re_423_> Number of previous, current selected restraints: 240132 244234 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160692 50938.176 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56354996 55034.176 53.744 make_re_422_> Number of previous, current restraints : 251752 253908 make_re_423_> Number of previous, current selected restraints: 244234 246390 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56354996 55034.176 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253908 254774 make_re_423_> Number of previous, current selected restraints: 246390 247256 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902352 70217.141 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73340004 71621.094 69.942 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254774 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 36.8677 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 : 10 0 0 0.022 0.022 1.2901 1.000 2 Bond angle potential : 15 0 0 3.465 3.465 3.2638 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.854 36.854 5.8611 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.167 1.167 0.68550E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 1 0.450 0.450 24.350 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.307 0.307 0.22216E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.979 7.979 0.96886E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 3.951 3.951 -0.20094 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.028 0.028 0.21613 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 31.672 35.768 1.8853 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 47 151 496 1472 3188 4229 4677 5770 7604 8897 9708 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254774 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 23 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 11.9782 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 : 10 0 0 0.005 0.005 0.53287E-01 1.000 2 Bond angle potential : 15 0 0 3.277 3.277 2.8897 1.000 3 Stereochemical cosine torsion poten: 23 0 0 38.566 38.566 5.3922 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.847 0.847 0.57653E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 23 0 0 0.319 0.319 -0.79934 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.263 1.263 0.37668E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 0.881 0.881 -0.20880E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 134.457 134.457 0.56275 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 92.367 92.367 1.2799 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 93.206 93.206 1.1646 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.545 29.442 1.3608 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3187 4229 4678 5769 7602 8897 9711 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:43:26 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372696 22824.898 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57682 66680 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712832 23157.062 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57684 66682 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872696 23313.180 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62926 72742 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872752 23313.234 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007696 23445.016 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62928 72744 18823 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167560 23601.133 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68170 78804 18823 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575696 23999.703 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68172 78806 18824 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68172 78806 18824 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68172 78806 20272 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735572 24155.832 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73415 84866 20272 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735628 24155.887 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73417 84868 20273 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73417 84868 20273 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189172 30458.176 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295640 30562.148 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303832 30570.148 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320216 30586.148 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31352984 30618.148 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385752 30650.148 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451288 30714.148 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484056 30746.148 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549592 30810.148 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582360 30842.148 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713432 30970.148 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31778968 31034.148 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910040 31162.148 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975576 31226.148 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237720 31482.148 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368792 31610.148 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630936 31866.148 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32762008 31994.148 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286296 32506.148 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548440 32762.148 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072728 33274.148 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334872 33530.148 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383448 34554.148 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907736 35066.148 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432024 35578.148 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480600 36602.148 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577752 38650.148 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626328 39674.148 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674904 40698.148 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772056 42746.148 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966360 46842.148 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063512 48890.148 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73417 79492 20077 Total number of restraints before, now : 0 227362 make_re_422_> Number of previous, current restraints : 0 227362 make_re_423_> Number of previous, current selected restraints: 0 227362 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063512 48890.148 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160680 50938.164 49.744 make_re_422_> Number of previous, current restraints : 227362 234670 make_re_423_> Number of previous, current selected restraints: 227362 234670 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160680 50938.164 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234670 241992 make_re_423_> Number of previous, current selected restraints: 234670 234474 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160680 50938.164 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241992 247648 make_re_423_> Number of previous, current selected restraints: 234474 240130 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160680 50938.164 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247648 251750 make_re_423_> Number of previous, current selected restraints: 240130 244232 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160680 50938.164 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56354984 55034.164 53.744 make_re_422_> Number of previous, current restraints : 251750 253906 make_re_423_> Number of previous, current selected restraints: 244232 246388 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56354984 55034.164 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253906 254773 make_re_423_> Number of previous, current selected restraints: 246388 247255 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902340 70217.125 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73339992 71621.086 69.942 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254773 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 25 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 37.7272 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 : 10 0 0 0.023 0.023 1.3593 1.000 2 Bond angle potential : 15 0 0 3.586 3.586 3.4394 1.000 3 Stereochemical cosine torsion poten: 23 0 1 36.389 36.389 5.6811 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.192 1.192 0.71569E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 25 0 1 0.440 0.440 25.363 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.230 0.230 0.12517E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.613 7.613 0.86615E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 2.988 2.988 -0.21512 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.42963E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.22251 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 30.995 34.832 1.6742 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 47 151 496 1472 3186 4229 4678 5769 7602 8897 9711 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254773 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 19 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 9.7125 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 : 10 0 0 0.005 0.005 0.64858E-01 1.000 2 Bond angle potential : 15 0 0 3.427 3.427 3.1690 1.000 3 Stereochemical cosine torsion poten: 23 0 0 33.106 33.106 5.1145 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.098 1.098 0.86498E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 19 0 0 0.294 0.294 -0.81992 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.398 0.398 0.37457E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 5.052 5.052 0.27274E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 132.543 132.543 0.55799 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.34413E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 2.684 2.684 0.23477 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 26.634 28.415 1.2393 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1472 3185 4229 4679 5767 7601 8897 9712 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 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 lars-bb 2.6.27-17-generic x86_64 Date and time of compilation : 2010/04/21 09:23:24 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2010/12/01 00:49:23 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 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 ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/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 ${MODINSTALL9v8}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 10694948 10444.285 10.199 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 10908232 10652.570 10.403 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 15040228 14687.723 14.343 mutate_mode_> Model residue 461 changed from GLU to LYS Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 15106424 14752.367 14.407 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 19238420 18787.520 18.347 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19292636 18840.465 18.399 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C +N atom indices : 3854 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 524 atom names : C CA +N O atom indices : 3854 3850 0 3855 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 0 0 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19452472 18996.555 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3883 5242 6060 1447 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19611528 19151.883 18.703 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3884 5244 6062 1448 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19665768 19204.852 18.755 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C +N atom indices : 7710 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1048 atom names : C CA +N O atom indices : 7710 7706 0 7711 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 5244 6062 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19825632 19360.969 18.907 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7767 10486 12122 2895 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19996328 19527.664 19.070 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7768 10488 12124 2896 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20050568 19580.633 19.122 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C +N atom indices : 11566 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 1572 atom names : C CA +N O atom indices : 11566 11562 0 11567 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 10488 12124 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20210432 19736.750 19.274 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11651 15730 18184 4343 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20355488 19878.406 19.413 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11652 15732 18186 4344 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20409728 19931.375 19.464 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C +N atom indices : 15422 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2096 atom names : C CA +N O atom indices : 15422 15418 0 15423 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 15732 18186 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20569592 20087.492 19.617 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15535 20974 24246 5791 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20778448 20291.453 19.816 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15536 20976 24248 5792 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20832688 20344.422 19.868 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C +N atom indices : 19278 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 2620 atom names : C CA +N O atom indices : 19278 19274 0 19279 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 20976 24248 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20992552 20500.539 20.020 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19419 26218 30308 7239 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21129288 20634.070 20.150 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19420 26220 30310 7240 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21183528 20687.039 20.202 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C +N atom indices : 23134 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3144 atom names : C CA +N O atom indices : 23134 23130 0 23135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 26220 30310 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21343392 20843.156 20.355 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23303 31462 36370 8687 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21507448 21003.367 20.511 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23304 31464 36372 8688 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21572520 21066.914 20.573 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C +N atom indices : 26990 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 3668 atom names : C CA +N O atom indices : 26990 26986 0 26991 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 31464 36372 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21732384 21223.031 20.726 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27187 36706 42432 10135 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21929240 21415.273 20.913 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27188 36708 42434 10136 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22007336 21491.539 20.988 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C +N atom indices : 30846 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4192 atom names : C CA +N O atom indices : 30846 30842 0 30847 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 36708 42434 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22167200 21647.656 21.140 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 31071 41950 48494 11583 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22403416 21878.336 21.366 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 31072 41952 48496 11584 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22497136 21969.859 21.455 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C +N atom indices : 34702 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 4716 atom names : C CA +N O atom indices : 34702 34698 0 34703 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 41952 48496 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22657000 22125.977 21.607 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34955 47194 54556 13031 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22940456 22402.789 21.878 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34956 47196 54558 13032 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C +N atom indices : 38558 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5240 atom names : C CA +N O atom indices : 38558 38554 0 38559 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 47196 54558 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100320 22558.906 22.030 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38839 52438 60618 14479 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23100376 22558.961 22.030 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38840 52440 60620 14480 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23212832 22668.781 22.137 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C +N atom indices : 42414 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 5764 atom names : C CA +N O atom indices : 42414 42410 0 42415 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 52440 60620 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23372696 22824.898 22.290 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42723 57682 66680 15927 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23712832 23157.062 22.614 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42724 57684 66682 15928 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C +N atom indices : 46270 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6288 atom names : C CA +N O atom indices : 46270 46266 0 46271 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 57684 66682 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872696 23313.180 22.767 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46607 62926 72742 17375 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23872752 23313.234 22.767 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46608 62928 72744 17376 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24007696 23445.016 22.896 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C +N atom indices : 50126 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 6812 atom names : C CA +N O atom indices : 50126 50122 0 50127 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 62928 72744 18823 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24167560 23601.133 23.048 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50491 68170 78804 18823 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24575696 23999.703 23.437 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68172 78806 18824 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50492 68172 78806 18824 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C +N atom indices : 53982 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 13 7336 atom names : C CA +N O atom indices : 53982 53978 0 53983 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 68172 78806 20271 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735560 24155.820 23.590 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54375 73414 84866 20271 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24735616 24155.875 23.590 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73416 84868 20272 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54376 73416 84868 20272 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: 53982 2 openf___224_> Open 1XCK_protein.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 31189160 30458.164 29.744 read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 # ALGNMT CODE 1 1XCK_protein.pdb 2 1XCK_protein.pdb openf___224_> Open 1XCK_protein.pdbLYS461.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS461.tmp read_mo_297_> Segments, residues, atoms: 14 7336 53984 read_mo_298_> Segment: 1 2 A 525 A 3856 read_mo_298_> Segment: 2 2 B 525 B 3856 read_mo_298_> Segment: 3 2 C 525 C 3856 read_mo_298_> Segment: 4 2 D 525 D 3856 read_mo_298_> Segment: 5 2 E 525 E 3856 read_mo_298_> Segment: 6 2 F 525 F 3856 read_mo_298_> Segment: 7 2 G 525 G 3856 read_mo_298_> Segment: 8 2 H 525 H 3856 read_mo_298_> Segment: 9 2 I 525 I 3856 read_mo_298_> Segment: 10 2 J 525 J 3856 read_mo_298_> Segment: 11 2 K 525 K 3856 read_mo_298_> Segment: 12 2 L 525 L 3856 read_mo_298_> Segment: 13 2 M 525 M 3856 read_mo_298_> Segment: 14 2 N 525 N 3856 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31295628 30562.137 29.846 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31303820 30570.137 29.854 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31320204 30586.137 29.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31352972 30618.137 29.901 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31385740 30650.137 29.932 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31451276 30714.137 29.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31484044 30746.137 30.026 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31549580 30810.137 30.088 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31582348 30842.137 30.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31713420 30970.137 30.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31778956 31034.137 30.307 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31910028 31162.137 30.432 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31975564 31226.137 30.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32237708 31482.137 30.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32368780 31610.137 30.869 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32630924 31866.137 31.119 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32761996 31994.137 31.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33286284 32506.137 31.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33548428 32762.137 31.994 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34072716 33274.137 32.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34334860 33530.137 32.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35383436 34554.137 33.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35907724 35066.137 34.244 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36432012 35578.137 34.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37480588 36602.137 35.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39577740 38650.137 37.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40626316 39674.137 38.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41674892 40698.137 39.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43772044 42746.137 41.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47966348 46842.137 45.744 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50063500 48890.137 47.744 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54376 73416 79492 20076 Total number of restraints before, now : 0 227360 make_re_422_> Number of previous, current restraints : 0 227360 make_re_423_> Number of previous, current selected restraints: 0 227360 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50063500 48890.137 47.744 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52160668 50938.152 49.744 make_re_422_> Number of previous, current restraints : 227360 234668 make_re_423_> Number of previous, current selected restraints: 227360 234668 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160668 50938.152 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v8}/modlib/omega.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 7518 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 234668 241990 make_re_423_> Number of previous, current selected restraints: 234668 234472 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160668 50938.152 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi1.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 241990 247646 make_re_423_> Number of previous, current selected restraints: 234472 240128 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160668 50938.152 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi2.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 247646 251748 make_re_423_> Number of previous, current selected restraints: 240128 244230 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52160668 50938.152 49.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/modlib/chi3.mdt getdata_643_> Protein accepted: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 56354972 55034.152 53.744 make_re_422_> Number of previous, current restraints : 251748 253904 make_re_423_> Number of previous, current selected restraints: 244230 246386 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56354972 55034.152 53.744 openf___224_> Open ${MODINSTALL9v8}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v8}/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: 1XCK_protein.pdb getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 253904 254772 make_re_423_> Number of previous, current selected restraints: 246386 247254 pick_re_612_> Number of MODEL atoms, selected restraints; 9 60 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71902328 70217.117 68.571 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73339980 71621.078 69.942 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254772 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 26 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 29.4521 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 : 10 0 0 0.021 0.021 1.2142 1.000 2 Bond angle potential : 15 0 0 3.550 3.550 3.3544 1.000 3 Stereochemical cosine torsion poten: 23 0 1 37.051 37.051 5.8485 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.954 0.954 0.46760E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 26 0 1 0.448 0.448 17.071 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.647 0.647 0.98702E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 7.699 7.699 0.88979E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.328 4.328 -0.19427 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.34081E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.000 0.000 0.21584 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 31.413 35.287 1.7623 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 152 496 1471 3185 4229 4679 5767 7601 8897 9712 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 7336 Number of all, selected real atoms : 53984 9 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 254772 60 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 22 Dynamic pairs routine : 5, NATM_SEL x NATM double loop 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 F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 12.7513 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 : 10 0 0 0.006 0.006 0.87078E-01 1.000 2 Bond angle potential : 15 0 0 3.463 3.463 3.2131 1.000 3 Stereochemical cosine torsion poten: 23 0 0 36.752 36.752 5.4666 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.049 1.049 0.80032E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 22 0 0 0.357 0.357 -0.45002 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 1.328 1.328 0.41622E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 15.831 15.831 0.42687 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 94.607 94.607 0.81896 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 72.322 72.322 1.6773 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.044 0.044 0.21630 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) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 25.712 29.103 1.1736 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1449 1456 2.295 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 5157751584 2.298 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 8 29 46 151 496 1471 3184 4229 4679 5767 7600 8895 9714 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984