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 slars-bb 2.6.35-22-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): 2010/12/02 16:39:29 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]: 10693576 10442.945 10.198 read_pd_459W> Residue type HID not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. 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 434 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]: 19290096 18837.984 18.396 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19449372 18993.527 18.548 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19608428 19148.855 18.700 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19662468 19201.629 18.752 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 7745 5228 6039 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19821784 19357.211 18.904 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10455 12076 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19992480 19523.906 19.066 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10457 12078 2881 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10457 12078 2881 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20046520 19576.680 19.118 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 11618 10457 12078 4321 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20205836 19732.262 19.270 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15684 18115 4321 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20350892 19873.918 19.408 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15686 18117 4322 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15686 18117 4322 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20404932 19926.691 19.460 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 15491 15686 18117 5762 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20564248 20082.273 19.612 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20913 24154 5762 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20773104 20286.234 19.811 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20915 24156 5763 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20915 24156 5763 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20827144 20339.008 19.862 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 19364 20915 24156 7203 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20986460 20494.590 20.014 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26142 30193 7203 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21123196 20628.121 20.145 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26144 30195 7204 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26144 30195 7204 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21177236 20680.895 20.196 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 23237 26144 30195 8644 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21336552 20836.477 20.348 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31371 36232 8644 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21500608 20996.688 20.505 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31373 36234 8645 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31373 36234 8645 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21565448 21060.008 20.566 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 27110 31373 36234 10085 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21724764 21215.590 20.718 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36600 42271 10085 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21921620 21407.832 20.906 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36602 42273 10086 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36602 42273 10086 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21999420 21483.809 20.980 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 30983 36602 42273 11526 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22158736 21639.391 21.132 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41829 48310 11526 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22394952 21870.070 21.357 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41831 48312 11527 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41831 48312 11527 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22488312 21961.242 21.447 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 34856 41831 48312 12967 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22647628 22116.824 21.598 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47058 54349 12967 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22647684 22116.879 21.599 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47060 54351 12968 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47060 54351 12968 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 38729 47060 54351 14408 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22807000 22272.461 21.750 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52287 60388 14408 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23090456 22549.273 22.021 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52289 60390 14409 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52289 60390 14409 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23202488 22658.680 22.128 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 42602 52289 60390 15849 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23361804 22814.262 22.280 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57516 66427 15849 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23701940 23146.426 22.604 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57518 66429 15850 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57518 66429 15850 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 46475 57518 66429 17290 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23861256 23302.008 22.756 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62745 72466 17290 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23861312 23302.062 22.756 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62747 72468 17291 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62747 72468 17291 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23995744 23433.344 22.884 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 50348 62747 72468 18731 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24155060 23588.926 23.036 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67974 78505 18731 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24563196 23987.496 23.425 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67976 78507 18732 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67976 78507 18732 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 54221 67976 78507 20172 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24722512 24143.078 23.577 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73203 84544 20172 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24722568 24143.133 23.577 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73205 84546 20173 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73205 84546 20173 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]: 31174740 30444.082 29.731 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31281208 30548.055 29.832 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31289400 30556.055 29.840 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31305784 30572.055 29.856 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31338552 30604.055 29.887 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31371320 30636.055 29.918 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31436856 30700.055 29.981 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31437176 30700.367 29.981 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31469944 30732.367 30.012 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31535480 30796.367 30.075 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31568248 30828.367 30.106 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31699320 30956.367 30.231 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31764856 31020.367 30.293 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31895928 31148.367 30.418 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31961464 31212.367 30.481 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32223608 31468.367 30.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32354680 31596.367 30.856 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32616824 31852.367 31.106 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32747896 31980.367 31.231 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33272184 32492.367 31.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33534328 32748.367 31.981 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34058616 33260.367 32.481 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34320760 33516.367 32.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35369336 34540.367 33.731 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35369736 34540.758 33.731 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35894024 35052.758 34.231 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36418312 35564.758 34.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37466888 36588.758 35.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39564040 38636.758 37.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40612616 39660.758 38.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41661192 40684.758 39.731 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43758344 42732.758 41.731 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43758904 42733.305 41.732 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47953208 46829.305 45.732 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50050360 48877.305 47.732 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73205 79170 19977 Total number of restraints before, now : 0 226574 make_re_422_> Number of previous, current restraints : 0 226574 make_re_423_> Number of previous, current selected restraints: 0 226574 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50050836 48877.770 47.732 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 make_re_422_> Number of previous, current restraints : 226574 233868 make_re_423_> Number of previous, current selected restraints: 226574 233868 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50050852 48877.785 47.732 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52148004 50925.785 49.732 make_re_422_> Number of previous, current restraints : 233868 241176 make_re_423_> Number of previous, current selected restraints: 233868 233686 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52148004 50925.785 49.732 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 : 241176 246818 make_re_423_> Number of previous, current selected restraints: 233686 239328 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52148004 50925.785 49.732 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 : 246818 250906 make_re_423_> Number of previous, current selected restraints: 239328 243416 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52148004 50925.785 49.732 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]: 56342308 55021.785 53.732 make_re_422_> Number of previous, current restraints : 250906 253062 make_re_423_> Number of previous, current selected restraints: 243416 245572 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56342308 55021.785 53.732 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 : 253062 253917 make_re_423_> Number of previous, current selected restraints: 245572 246427 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71889664 70204.750 68.559 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73327316 71608.703 69.930 >> 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 : 253917 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 34 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 : 13.3480 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 0.017 0.017 0.78785 1.000 2 Bond angle potential : 14 0 0 2.269 2.269 1.6482 1.000 3 Stereochemical cosine torsion poten: 18 0 0 47.232 47.232 3.1320 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.365 1.365 0.97822E-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 : 34 0 0 0.483 0.483 4.9743 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 1.849 1.849 0.80740E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 19.652 19.652 0.45549 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 125.681 125.681 2.5602 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.94489E-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 30.978 30.978 -0.69937 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3206 4250 4699 5789 7609 8906 9682 << 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 : 253917 54 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 : 4.8509 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 0.43388E-01 1.000 2 Bond angle potential : 14 0 0 1.650 1.650 0.76933 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.005 46.005 2.9266 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.109 1.109 0.12537 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 0.332 0.332 0.27816 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 3.375 3.375 0.26879 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 116.927 116.927 0.10802 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 132.676 132.676 0.79786 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.94805E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 2.361 2.361 0.23319 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 31.666 31.666 -0.79460 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3206 4249 4699 5787 7605 8905 9681 << 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 slars-bb 2.6.35-22-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): 2010/12/02 16:45:20 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048816 19578.922 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 11618 10456 12078 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208132 19734.504 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15683 18115 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353188 19876.160 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15685 18117 4321 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15685 18117 4321 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407228 19928.934 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 15491 15685 18117 5761 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566544 20084.516 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20912 24154 5761 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775400 20288.477 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20914 24156 5762 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20914 24156 5762 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829440 20341.250 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 19364 20914 24156 7202 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988756 20496.832 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26141 30193 7202 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125492 20630.363 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26143 30195 7203 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26143 30195 7203 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179532 20683.137 20.198 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 23237 26143 30195 8643 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338848 20838.719 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31370 36232 8643 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502904 20998.930 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31372 36234 8644 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31372 36234 8644 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567728 21062.234 20.569 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 27110 31372 36234 10084 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21727044 21217.816 20.721 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36599 42271 10084 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923900 21410.059 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36601 42273 10085 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36601 42273 10085 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001700 21486.035 20.982 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 30983 36601 42273 11525 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22161016 21641.617 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41828 48310 11525 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397232 21872.297 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41830 48312 11526 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41830 48312 11526 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490592 21963.469 21.449 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 34856 41830 48312 12966 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649908 22119.051 21.601 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47057 54349 12966 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649964 22119.105 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47059 54351 12967 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47059 54351 12967 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 38729 47059 54351 14407 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809280 22274.688 21.753 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52286 60388 14407 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092736 22551.500 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52288 60390 14408 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52288 60390 14408 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204768 22660.906 22.130 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 42602 52288 60390 15848 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23364084 22816.488 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57515 66427 15848 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704220 23148.652 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57517 66429 15849 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57517 66429 15849 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 46475 57517 66429 17289 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863536 23304.234 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62744 72466 17289 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863592 23304.289 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62746 72468 17290 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62746 72468 17290 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23998024 23435.570 22.886 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 50348 62746 72468 18730 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157340 23591.152 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67973 78505 18730 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565476 23989.723 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67975 78507 18731 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67975 78507 18731 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 54221 67975 78507 20171 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724792 24145.305 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73202 84544 20171 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724848 24145.359 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73204 84546 20172 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73204 84546 20172 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]: 31178392 30447.648 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284860 30551.621 29.836 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31293052 30559.621 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309436 30575.621 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31342204 30607.621 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374972 30639.621 29.922 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440508 30703.621 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440828 30703.934 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473596 30735.934 30.016 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31539132 30799.934 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571900 30831.934 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702972 30959.934 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768508 31023.934 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899580 31151.934 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31965116 31215.934 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227260 31471.934 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358332 31599.934 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620476 31855.934 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751548 31983.934 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275836 32495.934 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537980 32751.934 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062268 33263.934 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324412 33519.934 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372988 34543.934 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373388 34544.324 33.735 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897676 35056.324 34.235 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421964 35568.324 34.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470540 36592.324 35.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567692 38640.324 37.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616268 39664.324 38.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664844 40688.324 39.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761996 42736.324 41.735 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762556 42736.871 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956860 46832.871 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50054012 48880.871 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73204 79170 19976 Total number of restraints before, now : 0 226572 make_re_422_> Number of previous, current restraints : 0 226572 make_re_423_> Number of previous, current selected restraints: 0 226572 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50054012 48880.871 47.735 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 make_re_422_> Number of previous, current restraints : 226572 233866 make_re_423_> Number of previous, current selected restraints: 226572 233866 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50054028 48880.887 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52151180 50928.887 49.735 make_re_422_> Number of previous, current restraints : 233866 241174 make_re_423_> Number of previous, current selected restraints: 233866 233684 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151180 50928.887 49.735 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 : 241174 246816 make_re_423_> Number of previous, current selected restraints: 233684 239326 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151180 50928.887 49.735 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 : 246816 250904 make_re_423_> Number of previous, current selected restraints: 239326 243414 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151180 50928.887 49.735 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]: 56345484 55024.887 53.735 make_re_422_> Number of previous, current restraints : 250904 253060 make_re_423_> Number of previous, current selected restraints: 243414 245570 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345484 55024.887 53.735 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 : 253060 253916 make_re_423_> Number of previous, current selected restraints: 245570 246426 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892840 70207.852 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330492 71611.812 69.933 >> 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 : 253916 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 30.7215 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 0.016 0.016 0.70740 1.000 2 Bond angle potential : 14 0 0 2.226 2.226 1.5515 1.000 3 Stereochemical cosine torsion poten: 18 0 0 45.541 45.541 2.9419 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.229 1.229 0.76905E-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 : 35 0 3 0.579 0.579 23.171 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 1.685 1.685 0.66990E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 18.826 18.826 0.42025 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 126.533 126.533 2.7047 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 31.427 31.427 -1.2378 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 497 1511 3207 4249 4700 5786 7606 8905 9681 << 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 : 253916 54 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 : 4.2133 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 0.003 0.003 0.37141E-01 1.000 2 Bond angle potential : 14 0 0 1.845 1.845 0.90071 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.847 44.847 2.7793 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.057 1.057 0.12192 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 0.331 0.331 0.90329E-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 2.783 2.783 0.18281 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 114.730 114.730 0.87184E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 132.445 132.445 0.79837 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.94489E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.228 0.228 0.21818 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 32.547 32.547 -1.0971 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3204 4249 4701 5785 7604 8902 9680 << 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 slars-bb 2.6.35-22-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): 2010/12/02 16:51:06 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407200 19928.906 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 15491 15684 18117 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566516 20084.488 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20911 24154 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775372 20288.449 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20913 24156 5761 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20913 24156 5761 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829412 20341.223 19.864 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 19364 20913 24156 7201 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988728 20496.805 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26140 30193 7201 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125464 20630.336 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26142 30195 7202 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26142 30195 7202 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179504 20683.109 20.198 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 23237 26142 30195 8642 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338820 20838.691 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31369 36232 8642 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502876 20998.902 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31371 36234 8643 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31371 36234 8643 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567700 21062.207 20.569 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 27110 31371 36234 10083 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21727016 21217.789 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36598 42271 10083 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923872 21410.031 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36600 42273 10084 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36600 42273 10084 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001672 21486.008 20.982 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 30983 36600 42273 11524 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160988 21641.590 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41827 48310 11524 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397204 21872.270 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41829 48312 11525 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41829 48312 11525 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490564 21963.441 21.449 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 34856 41829 48312 12965 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649880 22119.023 21.601 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47056 54349 12965 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649936 22119.078 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47058 54351 12966 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47058 54351 12966 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 38729 47058 54351 14406 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809252 22274.660 21.753 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52285 60388 14406 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092708 22551.473 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52287 60390 14407 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52287 60390 14407 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204724 22660.863 22.130 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 42602 52287 60390 15847 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23364040 22816.445 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57514 66427 15847 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704176 23148.609 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57516 66429 15848 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57516 66429 15848 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 46475 57516 66429 17288 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863492 23304.191 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62743 72466 17288 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863548 23304.246 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62745 72468 17289 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62745 72468 17289 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997980 23435.527 22.886 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 50348 62745 72468 18729 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157296 23591.109 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67972 78505 18729 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565432 23989.680 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67974 78507 18730 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67974 78507 18730 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 54221 67974 78507 20170 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724748 24145.262 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73201 84544 20170 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724804 24145.316 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73203 84546 20171 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73203 84546 20171 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]: 31178348 30447.605 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284816 30551.578 29.836 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31293008 30559.578 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309392 30575.578 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31342160 30607.578 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374928 30639.578 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440464 30703.578 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440784 30703.891 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473552 30735.891 30.016 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31539088 30799.891 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571856 30831.891 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702928 30959.891 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768464 31023.891 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899536 31151.891 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31965072 31215.891 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227216 31471.891 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358288 31599.891 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620432 31855.891 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751504 31983.891 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275792 32495.891 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537936 32751.891 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062224 33263.891 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324368 33519.891 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372944 34543.891 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373344 34544.281 33.735 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897632 35056.281 34.235 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421920 35568.281 34.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470496 36592.281 35.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567648 38640.281 37.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616224 39664.281 38.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664800 40688.281 39.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761952 42736.281 41.735 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762512 42736.828 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956816 46832.828 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053968 48880.828 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73203 79170 19975 Total number of restraints before, now : 0 226570 make_re_422_> Number of previous, current restraints : 0 226570 make_re_423_> Number of previous, current selected restraints: 0 226570 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053968 48880.828 47.735 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 make_re_422_> Number of previous, current restraints : 226570 233864 make_re_423_> Number of previous, current selected restraints: 226570 233864 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053984 48880.844 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52151136 50928.844 49.735 make_re_422_> Number of previous, current restraints : 233864 241172 make_re_423_> Number of previous, current selected restraints: 233864 233682 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151136 50928.844 49.735 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 : 241172 246814 make_re_423_> Number of previous, current selected restraints: 233682 239324 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151136 50928.844 49.735 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 : 246814 250902 make_re_423_> Number of previous, current selected restraints: 239324 243412 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151136 50928.844 49.735 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]: 56345440 55024.844 53.735 make_re_422_> Number of previous, current restraints : 250902 253058 make_re_423_> Number of previous, current selected restraints: 243412 245568 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345440 55024.844 53.735 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 : 253058 253915 make_re_423_> Number of previous, current selected restraints: 245568 246425 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892796 70207.812 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330448 71611.766 69.933 >> 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 : 253915 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 37 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 : 37.8306 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 0.015 0.015 0.63807 1.000 2 Bond angle potential : 14 0 0 2.309 2.309 1.6957 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.426 46.426 3.0566 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.348 1.348 0.93600E-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 : 37 0 4 0.590 0.590 29.844 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 1.966 1.966 0.91227E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 20.388 20.388 0.48953 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 125.923 125.923 2.6010 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.034 0.034 0.94876E-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 31.525 31.525 -0.99000 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 498 1509 3206 4249 4703 5784 7603 8902 9681 << 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 : 253915 54 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 : 4.8597 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 0.36837E-01 1.000 2 Bond angle potential : 14 0 0 1.747 1.747 0.94852 1.000 3 Stereochemical cosine torsion poten: 18 0 0 47.220 47.220 3.1700 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.714 1.714 0.19432 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 0.342 0.342 0.35555 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 3.083 3.083 0.22438 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 107.517 107.517 0.14127 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 12.620 12.620 0.13099 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 7.316 7.316 0.16587 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 10.120 10.120 0.33467 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 32.399 32.399 -0.84265 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3204 4247 4703 5782 7601 8902 9678 << 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 slars-bb 2.6.35-22-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): 2010/12/02 16:56:57 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829384 20341.195 19.864 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 19364 20912 24156 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988700 20496.777 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26139 30193 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125436 20630.309 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26141 30195 7201 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26141 30195 7201 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179476 20683.082 20.198 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 23237 26141 30195 8641 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338792 20838.664 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31368 36232 8641 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502848 20998.875 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31370 36234 8642 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31370 36234 8642 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567672 21062.180 20.569 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 27110 31370 36234 10082 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726988 21217.762 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36597 42271 10082 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923844 21410.004 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36599 42273 10083 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36599 42273 10083 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001644 21485.980 20.982 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 30983 36599 42273 11523 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160960 21641.562 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41826 48310 11523 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397176 21872.242 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41828 48312 11524 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41828 48312 11524 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490520 21963.398 21.449 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 34856 41828 48312 12964 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649836 22118.980 21.601 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47055 54349 12964 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649892 22119.035 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47057 54351 12965 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47057 54351 12965 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 38729 47057 54351 14405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809208 22274.617 21.753 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52284 60388 14405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092664 22551.430 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52286 60390 14406 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52286 60390 14406 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204680 22660.820 22.130 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 42602 52286 60390 15846 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363996 22816.402 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57513 66427 15846 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704132 23148.566 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57515 66429 15847 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57515 66429 15847 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 46475 57515 66429 17287 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863448 23304.148 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62742 72466 17287 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863504 23304.203 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62744 72468 17288 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62744 72468 17288 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997920 23435.469 22.886 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 50348 62744 72468 18728 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157236 23591.051 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67971 78505 18728 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565372 23989.621 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67973 78507 18729 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67973 78507 18729 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 54221 67973 78507 20169 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724688 24145.203 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73200 84544 20169 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724744 24145.258 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73202 84546 20170 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73202 84546 20170 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]: 31178288 30447.547 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284756 30551.520 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292948 30559.520 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309332 30575.520 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31342100 30607.520 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374868 30639.520 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440404 30703.520 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440724 30703.832 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473492 30735.832 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31539028 30799.832 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571796 30831.832 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702868 30959.832 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768404 31023.832 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899476 31151.832 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31965012 31215.832 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227156 31471.832 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358228 31599.832 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620372 31855.832 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751444 31983.832 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275732 32495.832 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537876 32751.832 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062164 33263.832 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324308 33519.832 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372884 34543.832 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373284 34544.223 33.735 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897572 35056.223 34.235 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421860 35568.223 34.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470436 36592.223 35.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567588 38640.223 37.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616164 39664.223 38.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664740 40688.223 39.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761892 42736.223 41.735 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762452 42736.770 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956756 46832.770 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053908 48880.770 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73202 79170 19974 Total number of restraints before, now : 0 226568 make_re_422_> Number of previous, current restraints : 0 226568 make_re_423_> Number of previous, current selected restraints: 0 226568 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053908 48880.770 47.735 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 make_re_422_> Number of previous, current restraints : 226568 233862 make_re_423_> Number of previous, current selected restraints: 226568 233862 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053924 48880.785 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52151076 50928.785 49.735 make_re_422_> Number of previous, current restraints : 233862 241170 make_re_423_> Number of previous, current selected restraints: 233862 233680 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151076 50928.785 49.735 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 : 241170 246812 make_re_423_> Number of previous, current selected restraints: 233680 239322 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151076 50928.785 49.735 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 : 246812 250900 make_re_423_> Number of previous, current selected restraints: 239322 243410 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151076 50928.785 49.735 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]: 56345380 55024.785 53.735 make_re_422_> Number of previous, current restraints : 250900 253056 make_re_423_> Number of previous, current selected restraints: 243410 245566 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345380 55024.785 53.735 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 : 253056 253914 make_re_423_> Number of previous, current selected restraints: 245566 246424 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892736 70207.750 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330388 71611.703 69.933 >> 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 : 253914 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 23.5751 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 0.015 0.015 0.61241 1.000 2 Bond angle potential : 14 0 0 2.308 2.308 1.7018 1.000 3 Stereochemical cosine torsion poten: 18 0 0 47.042 47.042 3.1253 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.539 1.539 0.12441 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 35 0 1 0.554 0.554 15.146 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 2.139 2.139 0.10804 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 20.078 20.078 0.47490 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 126.160 126.160 2.6411 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 32.545 32.545 -0.67797 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1510 3205 4249 4703 5783 7600 8902 9678 << 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 : 253914 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 38 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 : 5.9911 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 0.34787E-01 1.000 2 Bond angle potential : 14 0 0 1.656 1.656 0.76119 1.000 3 Stereochemical cosine torsion poten: 18 0 0 49.475 49.475 3.1581 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.223 1.223 0.14811 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 38 0 0 0.379 0.379 0.89813E-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 3.596 3.596 0.30523 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 16.298 16.298 0.32966 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 101.462 101.462 0.36668 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 79.029 79.029 1.3579 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 12.244 12.244 0.31384 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 33.321 33.321 -0.87424 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3204 4246 4704 5781 7599 8903 9680 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:03:07 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179448 20683.055 20.198 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 23237 26140 30195 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338764 20838.637 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31367 36232 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502820 20998.848 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31369 36234 8641 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31369 36234 8641 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567644 21062.152 20.569 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 27110 31369 36234 10081 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726960 21217.734 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36596 42271 10081 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923816 21409.977 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36598 42273 10082 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36598 42273 10082 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001600 21485.938 20.982 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 30983 36598 42273 11522 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160916 21641.520 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41825 48310 11522 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397132 21872.199 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41827 48312 11523 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41827 48312 11523 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490476 21963.355 21.449 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 34856 41827 48312 12963 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649792 22118.938 21.601 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47054 54349 12963 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649848 22118.992 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47056 54351 12964 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47056 54351 12964 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 38729 47056 54351 14404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809164 22274.574 21.753 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52283 60388 14404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092620 22551.387 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52285 60390 14405 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52285 60390 14405 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204636 22660.777 22.130 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 42602 52285 60390 15845 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363952 22816.359 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57512 66427 15845 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704088 23148.523 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57514 66429 15846 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57514 66429 15846 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 46475 57514 66429 17286 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863404 23304.105 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62741 72466 17286 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863460 23304.160 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62743 72468 17287 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62743 72468 17287 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997876 23435.426 22.886 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 50348 62743 72468 18727 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157192 23591.008 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67970 78505 18727 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565328 23989.578 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67972 78507 18728 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67972 78507 18728 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 54221 67972 78507 20168 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724644 24145.160 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73199 84544 20168 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724700 24145.215 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73201 84546 20169 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73201 84546 20169 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]: 31178244 30447.504 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284712 30551.477 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292904 30559.477 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309288 30575.477 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31342056 30607.477 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374824 30639.477 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440360 30703.477 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440680 30703.789 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473448 30735.789 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538984 30799.789 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571752 30831.789 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702824 30959.789 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768360 31023.789 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899432 31151.789 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964968 31215.789 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227112 31471.789 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358184 31599.789 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620328 31855.789 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751400 31983.789 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275688 32495.789 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537832 32751.789 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062120 33263.789 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324264 33519.789 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372840 34543.789 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373240 34544.180 33.735 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897528 35056.180 34.235 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421816 35568.180 34.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470392 36592.180 35.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567544 38640.180 37.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616120 39664.180 38.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664696 40688.180 39.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761848 42736.180 41.735 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762408 42736.727 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956712 46832.727 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053864 48880.727 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73201 79170 19973 Total number of restraints before, now : 0 226566 make_re_422_> Number of previous, current restraints : 0 226566 make_re_423_> Number of previous, current selected restraints: 0 226566 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053864 48880.727 47.735 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 make_re_422_> Number of previous, current restraints : 226566 233860 make_re_423_> Number of previous, current selected restraints: 226566 233860 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053880 48880.742 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52151032 50928.742 49.735 make_re_422_> Number of previous, current restraints : 233860 241168 make_re_423_> Number of previous, current selected restraints: 233860 233678 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151032 50928.742 49.735 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 : 241168 246810 make_re_423_> Number of previous, current selected restraints: 233678 239320 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151032 50928.742 49.735 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 : 246810 250898 make_re_423_> Number of previous, current selected restraints: 239320 243408 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52151032 50928.742 49.735 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]: 56345336 55024.742 53.735 make_re_422_> Number of previous, current restraints : 250898 253054 make_re_423_> Number of previous, current selected restraints: 243408 245564 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345336 55024.742 53.735 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 : 253054 253913 make_re_423_> Number of previous, current selected restraints: 245564 246423 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892692 70207.703 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330344 71611.664 69.933 >> 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 : 253913 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 18.1125 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 0.015 0.015 0.67844 1.000 2 Bond angle potential : 14 0 0 2.208 2.208 1.5385 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.535 46.535 3.0330 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.152 1.152 0.66795E-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 : 35 0 1 0.530 0.530 10.397 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 1.877 1.877 0.83186E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 18.225 18.225 0.39641 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 124.942 124.942 2.4383 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.10326 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 31.822 31.822 -0.84526 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3205 4247 4705 5783 7597 8904 9680 << 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 : 253913 54 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 : 5.7016 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 0.003 0.003 0.25809E-01 1.000 2 Bond angle potential : 14 0 0 1.897 1.897 0.92079 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.935 44.935 2.8453 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.266 1.266 0.16522 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 0.336 0.336 0.15711 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 3.368 3.368 0.26773 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 114.607 114.607 0.86552E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 130.675 130.675 0.81181 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.94489E-01 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 107.771 107.771 1.0957 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 33.004 33.004 -0.76883 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3203 4245 4705 5780 7596 8902 9681 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:08:59 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726932 21217.707 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36595 42271 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923788 21409.949 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36597 42273 10081 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36597 42273 10081 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001572 21485.910 20.982 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 30983 36597 42273 11521 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160888 21641.492 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41824 48310 11521 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397104 21872.172 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41826 48312 11522 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41826 48312 11522 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490448 21963.328 21.449 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 34856 41826 48312 12962 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649764 22118.910 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47053 54349 12962 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649820 22118.965 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47055 54351 12963 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47055 54351 12963 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 38729 47055 54351 14403 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809136 22274.547 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52282 60388 14403 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092592 22551.359 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52284 60390 14404 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52284 60390 14404 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204592 22660.734 22.130 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 42602 52284 60390 15844 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363908 22816.316 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57511 66427 15844 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704044 23148.480 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57513 66429 15845 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57513 66429 15845 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 46475 57513 66429 17285 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863360 23304.062 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62740 72466 17285 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863416 23304.117 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62742 72468 17286 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62742 72468 17286 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997816 23435.367 22.886 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 50348 62742 72468 18726 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157132 23590.949 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67969 78505 18726 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565268 23989.520 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67971 78507 18727 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67971 78507 18727 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 54221 67971 78507 20167 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724584 24145.102 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73198 84544 20167 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724640 24145.156 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73200 84546 20168 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73200 84546 20168 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]: 31178184 30447.445 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284652 30551.418 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292844 30559.418 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309228 30575.418 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341996 30607.418 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374764 30639.418 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440300 30703.418 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440620 30703.730 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473388 30735.730 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538924 30799.730 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571692 30831.730 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702764 30959.730 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768300 31023.730 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899372 31151.730 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964908 31215.730 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227052 31471.730 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358124 31599.730 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620268 31855.730 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751340 31983.730 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275628 32495.730 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537772 32751.730 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062060 33263.730 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324204 33519.730 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372780 34543.730 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373180 34544.121 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897468 35056.121 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421756 35568.121 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470332 36592.121 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567484 38640.121 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616060 39664.121 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664636 40688.121 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761788 42736.121 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762348 42736.668 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956652 46832.668 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053804 48880.668 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73200 79170 19972 Total number of restraints before, now : 0 226564 make_re_422_> Number of previous, current restraints : 0 226564 make_re_423_> Number of previous, current selected restraints: 0 226564 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053804 48880.668 47.735 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 make_re_422_> Number of previous, current restraints : 226564 233858 make_re_423_> Number of previous, current selected restraints: 226564 233858 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053820 48880.684 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150972 50928.684 49.735 make_re_422_> Number of previous, current restraints : 233858 241166 make_re_423_> Number of previous, current selected restraints: 233858 233676 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150972 50928.684 49.735 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 : 241166 246808 make_re_423_> Number of previous, current selected restraints: 233676 239318 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150972 50928.684 49.735 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 : 246808 250896 make_re_423_> Number of previous, current selected restraints: 239318 243406 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150972 50928.684 49.735 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]: 56345276 55024.684 53.735 make_re_422_> Number of previous, current restraints : 250896 253052 make_re_423_> Number of previous, current selected restraints: 243406 245562 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345276 55024.684 53.735 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 : 253052 253912 make_re_423_> Number of previous, current selected restraints: 245562 246422 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892632 70207.648 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330284 71611.609 69.933 >> 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 : 253912 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 34 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 : 10.5584 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 0.017 0.017 0.77759 1.000 2 Bond angle potential : 14 0 0 2.108 2.108 1.4024 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.004 46.004 3.0007 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.339 1.339 0.91905E-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 : 34 0 0 0.433 0.433 2.7819 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 1.829 1.829 0.78942E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 19.338 19.338 0.44175 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 126.153 126.153 2.6398 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 31.929 31.929 -0.98224 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3203 4245 4705 5779 7597 8902 9682 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 53984 9 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. conmin__610W> Precision problem; starting from scratch. >> 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 : 253912 54 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 : 6.9138 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 0.39944E-01 1.000 2 Bond angle potential : 14 0 0 1.952 1.952 1.0288 1.000 3 Stereochemical cosine torsion poten: 18 0 0 52.949 52.949 3.1950 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.575 1.575 0.17858 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 0.346 0.346 0.27183 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 3.013 3.013 0.21422 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 124.285 124.285 1.5163 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 3.672 3.672 -0.13701 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 108.590 108.590 1.0304 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 33.049 33.049 -0.64057 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3202 4244 4706 5779 7593 8901 9679 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:14:47 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160876 21641.480 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41823 48310 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397092 21872.160 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41825 48312 11521 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41825 48312 11521 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490436 21963.316 21.449 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 34856 41825 48312 12961 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649752 22118.898 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47052 54349 12961 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649808 22118.953 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47054 54351 12962 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47054 54351 12962 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 38729 47054 54351 14402 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809124 22274.535 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52281 60388 14402 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092580 22551.348 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52283 60390 14403 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52283 60390 14403 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204580 22660.723 22.130 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 42602 52283 60390 15843 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363896 22816.305 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57510 66427 15843 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704032 23148.469 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57512 66429 15844 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57512 66429 15844 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 46475 57512 66429 17284 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863348 23304.051 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62739 72466 17284 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863404 23304.105 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62741 72468 17285 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62741 72468 17285 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997804 23435.355 22.886 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 50348 62741 72468 18725 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157120 23590.938 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67968 78505 18725 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565256 23989.508 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67970 78507 18726 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67970 78507 18726 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 54221 67970 78507 20166 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724572 24145.090 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73197 84544 20166 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724628 24145.145 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73199 84546 20167 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73199 84546 20167 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]: 31178172 30447.434 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284640 30551.406 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292832 30559.406 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309216 30575.406 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341984 30607.406 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374752 30639.406 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440288 30703.406 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440608 30703.719 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473376 30735.719 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538912 30799.719 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571680 30831.719 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702752 30959.719 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768288 31023.719 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899360 31151.719 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964896 31215.719 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227040 31471.719 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358112 31599.719 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620256 31855.719 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751328 31983.719 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275616 32495.719 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537760 32751.719 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062048 33263.719 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324192 33519.719 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372768 34543.719 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373168 34544.109 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897456 35056.109 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421744 35568.109 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470320 36592.109 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567472 38640.109 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616048 39664.109 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664624 40688.109 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761776 42736.109 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762336 42736.656 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956640 46832.656 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053792 48880.656 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73199 79170 19971 Total number of restraints before, now : 0 226562 make_re_422_> Number of previous, current restraints : 0 226562 make_re_423_> Number of previous, current selected restraints: 0 226562 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053792 48880.656 47.735 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 make_re_422_> Number of previous, current restraints : 226562 233856 make_re_423_> Number of previous, current selected restraints: 226562 233856 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053808 48880.672 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150960 50928.672 49.735 make_re_422_> Number of previous, current restraints : 233856 241164 make_re_423_> Number of previous, current selected restraints: 233856 233674 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150960 50928.672 49.735 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 : 241164 246806 make_re_423_> Number of previous, current selected restraints: 233674 239316 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150960 50928.672 49.735 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 : 246806 250894 make_re_423_> Number of previous, current selected restraints: 239316 243404 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150960 50928.672 49.735 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]: 56345264 55024.672 53.735 make_re_422_> Number of previous, current restraints : 250894 253050 make_re_423_> Number of previous, current selected restraints: 243404 245560 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345264 55024.672 53.735 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 : 253050 253911 make_re_423_> Number of previous, current selected restraints: 245560 246421 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892620 70207.641 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330272 71611.594 69.933 >> 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 : 253911 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 25.3349 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 0.017 0.017 0.78030 1.000 2 Bond angle potential : 14 0 0 2.160 2.160 1.4770 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.388 46.388 3.0351 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.291 1.291 0.84233E-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 : 35 0 3 0.558 0.558 17.576 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 1.825 1.825 0.78637E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 19.117 19.117 0.43230 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 125.483 125.483 2.5273 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 31.335 31.335 -0.97506 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1510 3204 4245 4706 5778 7593 8903 9679 << 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 : 253911 54 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 : 4.1255 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 0.33862E-01 1.000 2 Bond angle potential : 14 0 0 2.272 2.272 1.2974 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.180 44.180 2.7280 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.470 1.470 0.21160 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 0.339 0.339 -0.59592E-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 3.444 3.444 0.27993 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 3.634 3.634 0.14701 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 4.995 4.995 -0.11247 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 2.800 2.800 0.12221 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 32.933 32.933 -0.73819 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3202 4242 4707 5777 7592 8900 9679 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:20:39 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12960 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649740 22118.887 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47051 54349 12960 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649796 22118.941 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47053 54351 12961 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47053 54351 12961 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 38729 47053 54351 14401 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809112 22274.523 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52280 60388 14401 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092568 22551.336 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52282 60390 14402 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52282 60390 14402 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204568 22660.711 22.130 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 42602 52282 60390 15842 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363884 22816.293 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57509 66427 15842 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704020 23148.457 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57511 66429 15843 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57511 66429 15843 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 46475 57511 66429 17283 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863336 23304.039 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62738 72466 17283 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863392 23304.094 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62740 72468 17284 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62740 72468 17284 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997792 23435.344 22.886 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 50348 62740 72468 18724 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157108 23590.926 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67967 78505 18724 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565244 23989.496 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67969 78507 18725 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67969 78507 18725 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 54221 67969 78507 20165 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724560 24145.078 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73196 84544 20165 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724616 24145.133 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73198 84546 20166 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73198 84546 20166 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]: 31178160 30447.422 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284628 30551.395 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292820 30559.395 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309204 30575.395 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341972 30607.395 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374740 30639.395 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440276 30703.395 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440596 30703.707 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473364 30735.707 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538900 30799.707 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571668 30831.707 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702740 30959.707 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768276 31023.707 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899348 31151.707 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964884 31215.707 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227028 31471.707 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358100 31599.707 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620244 31855.707 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751316 31983.707 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275604 32495.707 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537748 32751.707 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062036 33263.707 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324180 33519.707 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372756 34543.707 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373156 34544.098 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897444 35056.098 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421732 35568.098 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470308 36592.098 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567460 38640.098 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616036 39664.098 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664612 40688.098 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761764 42736.098 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762324 42736.645 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956628 46832.645 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053780 48880.645 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73198 79170 19970 Total number of restraints before, now : 0 226560 make_re_422_> Number of previous, current restraints : 0 226560 make_re_423_> Number of previous, current selected restraints: 0 226560 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053780 48880.645 47.735 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 make_re_422_> Number of previous, current restraints : 226560 233854 make_re_423_> Number of previous, current selected restraints: 226560 233854 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053796 48880.660 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150948 50928.660 49.735 make_re_422_> Number of previous, current restraints : 233854 241162 make_re_423_> Number of previous, current selected restraints: 233854 233672 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150948 50928.660 49.735 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 : 241162 246804 make_re_423_> Number of previous, current selected restraints: 233672 239314 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150948 50928.660 49.735 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 : 246804 250892 make_re_423_> Number of previous, current selected restraints: 239314 243402 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150948 50928.660 49.735 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]: 56345252 55024.660 53.735 make_re_422_> Number of previous, current restraints : 250892 253048 make_re_423_> Number of previous, current selected restraints: 243402 245558 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345252 55024.660 53.735 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 : 253048 253910 make_re_423_> Number of previous, current selected restraints: 245558 246420 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892608 70207.625 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330260 71611.578 69.933 >> 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 : 253910 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 30 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 : 10.1007 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 0.017 0.017 0.82887 1.000 2 Bond angle potential : 14 0 0 2.342 2.342 1.7699 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.203 44.203 2.7843 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.125 1.125 0.65940E-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 : 30 0 0 0.427 0.427 3.0286 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 1.656 1.656 0.64691E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 16.907 16.907 0.34925 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 125.545 125.545 2.5377 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 28.564 28.564 -1.6543 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3202 4242 4707 5775 7591 8900 9679 << 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 : 253910 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 29 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 : 5.4127 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 0.13273 1.000 2 Bond angle potential : 14 0 0 2.404 2.404 1.5339 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.956 46.956 2.7447 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.905 0.905 0.87272E-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 : 29 0 0 0.367 0.367 -0.25852E-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 2.485 2.485 0.14580 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 6.415 6.415 0.16082 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 95.402 95.402 0.37136 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 73.173 73.173 1.5074 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 29.528 29.528 -1.4614 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3200 4242 4708 5776 7589 8899 9678 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:26:31 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809100 22274.512 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52279 60388 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092556 22551.324 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52281 60390 14401 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52281 60390 14401 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204556 22660.699 22.130 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 42602 52281 60390 15841 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363872 22816.281 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57508 66427 15841 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23704008 23148.445 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57510 66429 15842 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57510 66429 15842 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 46475 57510 66429 17282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863324 23304.027 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62737 72466 17282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863380 23304.082 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62739 72468 17283 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62739 72468 17283 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997780 23435.332 22.886 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 50348 62739 72468 18723 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157096 23590.914 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67966 78505 18723 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565232 23989.484 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67968 78507 18724 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67968 78507 18724 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 54221 67968 78507 20164 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724548 24145.066 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73195 84544 20164 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724604 24145.121 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73197 84546 20165 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73197 84546 20165 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]: 31178148 30447.410 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284616 30551.383 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292808 30559.383 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309192 30575.383 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341960 30607.383 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374728 30639.383 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440264 30703.383 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440584 30703.695 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473352 30735.695 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538888 30799.695 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571656 30831.695 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702728 30959.695 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768264 31023.695 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899336 31151.695 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964872 31215.695 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227016 31471.695 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358088 31599.695 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620232 31855.695 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751304 31983.695 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275592 32495.695 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537736 32751.695 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062024 33263.695 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324168 33519.695 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372744 34543.695 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373144 34544.086 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897432 35056.086 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421720 35568.086 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470296 36592.086 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567448 38640.086 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616024 39664.086 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664600 40688.086 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761752 42736.086 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762312 42736.633 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956616 46832.633 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053768 48880.633 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73197 79170 19969 Total number of restraints before, now : 0 226558 make_re_422_> Number of previous, current restraints : 0 226558 make_re_423_> Number of previous, current selected restraints: 0 226558 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053768 48880.633 47.735 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 make_re_422_> Number of previous, current restraints : 226558 233852 make_re_423_> Number of previous, current selected restraints: 226558 233852 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053784 48880.648 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150936 50928.648 49.735 make_re_422_> Number of previous, current restraints : 233852 241160 make_re_423_> Number of previous, current selected restraints: 233852 233670 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150936 50928.648 49.735 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 : 241160 246802 make_re_423_> Number of previous, current selected restraints: 233670 239312 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150936 50928.648 49.735 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 : 246802 250890 make_re_423_> Number of previous, current selected restraints: 239312 243400 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150936 50928.648 49.735 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]: 56345240 55024.648 53.735 make_re_422_> Number of previous, current restraints : 250890 253046 make_re_423_> Number of previous, current selected restraints: 243400 245556 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345240 55024.648 53.735 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 : 253046 253909 make_re_423_> Number of previous, current selected restraints: 245556 246419 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892596 70207.609 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330248 71611.570 69.933 >> 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 : 253909 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 44.3833 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 0.017 0.017 0.81057 1.000 2 Bond angle potential : 14 0 0 2.463 2.463 1.9383 1.000 3 Stereochemical cosine torsion poten: 18 0 0 43.891 43.891 2.7740 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.275 1.275 0.84738E-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 : 35 0 3 0.564 0.564 36.726 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 1.676 1.676 0.66301E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 17.450 17.450 0.36788 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 127.293 127.293 2.8367 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.034 0.034 0.94876E-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 28.741 28.741 -1.5321 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 152 497 1510 3200 4242 4706 5775 7589 8899 9677 << 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 : 253909 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 28 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 : 9.2173 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 0.010 0.010 0.25655 1.000 2 Bond angle potential : 14 0 0 3.250 3.250 2.6121 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.510 46.510 2.9999 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.069 1.069 0.11560 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 28 0 0 0.392 0.392 0.21049 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 2.890 2.890 0.19713 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 32.468 32.468 1.5092 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 135.232 135.232 0.81102 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 66.927 66.927 1.6662 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 4.721 4.721 0.24575 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 29.830 29.830 -1.4066 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3198 4240 4709 5775 7588 8898 9675 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:32:20 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15840 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363860 22816.270 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57507 66427 15840 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703996 23148.434 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57509 66429 15841 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57509 66429 15841 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 46475 57509 66429 17281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863312 23304.016 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62736 72466 17281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863368 23304.070 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62738 72468 17282 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62738 72468 17282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997768 23435.320 22.886 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 50348 62738 72468 18722 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157084 23590.902 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67965 78505 18722 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565220 23989.473 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67967 78507 18723 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67967 78507 18723 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 54221 67967 78507 20163 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724536 24145.055 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73194 84544 20163 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724592 24145.109 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73196 84546 20164 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73196 84546 20164 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]: 31178136 30447.398 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284604 30551.371 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292796 30559.371 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309180 30575.371 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341948 30607.371 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374716 30639.371 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440252 30703.371 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440572 30703.684 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473340 30735.684 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538876 30799.684 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571644 30831.684 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702716 30959.684 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768252 31023.684 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899324 31151.684 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964860 31215.684 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227004 31471.684 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358076 31599.684 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620220 31855.684 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751292 31983.684 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275580 32495.684 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537724 32751.684 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062012 33263.684 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324156 33519.684 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372732 34543.684 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373132 34544.074 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897420 35056.074 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421708 35568.074 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470284 36592.074 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567436 38640.074 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616012 39664.074 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664588 40688.074 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761740 42736.074 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762300 42736.621 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956604 46832.621 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053756 48880.621 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73196 79170 19968 Total number of restraints before, now : 0 226556 make_re_422_> Number of previous, current restraints : 0 226556 make_re_423_> Number of previous, current selected restraints: 0 226556 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053756 48880.621 47.735 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 make_re_422_> Number of previous, current restraints : 226556 233850 make_re_423_> Number of previous, current selected restraints: 226556 233850 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053772 48880.637 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150924 50928.637 49.735 make_re_422_> Number of previous, current restraints : 233850 241158 make_re_423_> Number of previous, current selected restraints: 233850 233668 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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 : 241158 246800 make_re_423_> Number of previous, current selected restraints: 233668 239310 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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 : 246800 250888 make_re_423_> Number of previous, current selected restraints: 239310 243398 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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]: 56345228 55024.637 53.735 make_re_422_> Number of previous, current restraints : 250888 253044 make_re_423_> Number of previous, current selected restraints: 243398 245554 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345228 55024.637 53.735 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 : 253044 253908 make_re_423_> Number of previous, current selected restraints: 245554 246418 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892584 70207.602 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330236 71611.562 69.933 >> 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 : 253908 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 41 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 : 336.6364 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 0.016 0.016 0.67556 1.000 2 Bond angle potential : 14 0 0 2.324 2.324 1.7542 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.544 44.544 2.8012 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.258 1.258 0.83651E-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 : 41 0 5 0.725 0.725 329.78 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 1.421 1.421 0.47646E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 16.075 16.075 0.32282 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 124.297 124.297 2.3344 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 29.703 29.703 -1.4903 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1475037888 2.134 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 1 22 30 88 152 496 1509 3199 4240 4710 5774 7587 8898 9674 << 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 : 253908 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 42 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 : 10.1763 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 0.65422E-01 1.000 2 Bond angle potential : 14 0 0 2.454 2.454 1.6438 1.000 3 Stereochemical cosine torsion poten: 18 0 0 47.269 47.269 2.8153 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.046 1.046 0.11809 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 42 0 0 0.501 0.501 4.2034 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 2.485 2.485 0.14574 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 14.513 14.513 0.27963 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 106.276 106.276 0.51074 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 78.823 78.823 1.3624 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 14.463 14.463 0.34653 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 30.782 30.782 -1.3148 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3197 4239 4710 5778 7582 8900 9674 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:38:13 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15840 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363860 22816.270 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57507 66427 15840 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703996 23148.434 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57509 66429 15841 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57509 66429 15841 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 46475 57509 66429 17281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863312 23304.016 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62736 72466 17281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863368 23304.070 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62738 72468 17282 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62738 72468 17282 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997768 23435.320 22.886 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 50348 62738 72468 18722 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157084 23590.902 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67965 78505 18722 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565220 23989.473 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67967 78507 18723 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67967 78507 18723 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 54221 67967 78507 20163 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724536 24145.055 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73194 84544 20163 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724592 24145.109 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73196 84546 20164 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73196 84546 20164 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]: 31178136 30447.398 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284604 30551.371 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292796 30559.371 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309180 30575.371 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341948 30607.371 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374716 30639.371 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440252 30703.371 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440572 30703.684 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473340 30735.684 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538876 30799.684 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571644 30831.684 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702716 30959.684 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768252 31023.684 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899324 31151.684 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964860 31215.684 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32227004 31471.684 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358076 31599.684 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620220 31855.684 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751292 31983.684 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275580 32495.684 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537724 32751.684 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062012 33263.684 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324156 33519.684 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372732 34543.684 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373132 34544.074 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897420 35056.074 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421708 35568.074 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470284 36592.074 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567436 38640.074 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616012 39664.074 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664588 40688.074 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761740 42736.074 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762300 42736.621 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956604 46832.621 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053756 48880.621 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73196 79170 19968 Total number of restraints before, now : 0 226556 make_re_422_> Number of previous, current restraints : 0 226556 make_re_423_> Number of previous, current selected restraints: 0 226556 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053756 48880.621 47.735 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 make_re_422_> Number of previous, current restraints : 226556 233850 make_re_423_> Number of previous, current selected restraints: 226556 233850 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053772 48880.637 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150924 50928.637 49.735 make_re_422_> Number of previous, current restraints : 233850 241158 make_re_423_> Number of previous, current selected restraints: 233850 233668 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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 : 241158 246800 make_re_423_> Number of previous, current selected restraints: 233668 239310 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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 : 246800 250888 make_re_423_> Number of previous, current selected restraints: 239310 243398 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150924 50928.637 49.735 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]: 56345228 55024.637 53.735 make_re_422_> Number of previous, current restraints : 250888 253044 make_re_423_> Number of previous, current selected restraints: 243398 245554 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345228 55024.637 53.735 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 : 253044 253908 make_re_423_> Number of previous, current selected restraints: 245554 246418 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892584 70207.602 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330236 71611.562 69.933 >> 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 : 253908 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 28 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 : 8.9287 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 0.010 0.010 0.25340 1.000 2 Bond angle potential : 14 0 0 3.257 3.257 2.6230 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.508 46.508 2.9978 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.064 1.064 0.11454 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 28 0 0 0.392 0.392 0.20911 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 2.876 2.876 0.19529 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 32.463 32.463 1.3475 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 135.291 135.291 0.62056 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 66.988 66.988 1.7274 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 4.742 4.742 0.24587 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 29.828 29.828 -1.4058 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3197 4239 4710 5778 7582 8900 9674 << 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 : 253908 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 28 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 : 8.9115 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 0.010 0.010 0.26755 1.000 2 Bond angle potential : 14 0 0 3.197 3.197 2.5473 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.721 46.721 3.0169 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.976 0.976 0.10086 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 28 0 0 0.397 0.397 0.32068 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 2.869 2.869 0.19425 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 32.399 32.399 1.3395 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 134.054 134.054 0.60954 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 67.920 67.920 1.7018 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 5.676 5.676 0.25167 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 29.740 29.740 -1.4385 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3197 4239 4710 5778 7582 8900 9676 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:44:52 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363848 22816.258 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57506 66427 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703984 23148.422 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 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 46475 57508 66429 17280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863300 23304.004 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62735 72466 17280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863356 23304.059 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62737 72468 17281 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62737 72468 17281 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997756 23435.309 22.886 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 50348 62737 72468 18721 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157072 23590.891 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67964 78505 18721 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565208 23989.461 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67966 78507 18722 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67966 78507 18722 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 54221 67966 78507 20162 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724524 24145.043 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73193 84544 20162 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724580 24145.098 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73195 84546 20163 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73195 84546 20163 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]: 31178124 30447.387 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284592 30551.359 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292784 30559.359 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309168 30575.359 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341936 30607.359 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374704 30639.359 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440240 30703.359 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440560 30703.672 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473328 30735.672 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538864 30799.672 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571632 30831.672 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702704 30959.672 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768240 31023.672 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899312 31151.672 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964848 31215.672 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32226992 31471.672 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358064 31599.672 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620208 31855.672 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751280 31983.672 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275568 32495.672 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537712 32751.672 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34062000 33263.672 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324144 33519.672 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372720 34543.672 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373120 34544.062 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897408 35056.062 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421696 35568.062 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470272 36592.062 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567424 38640.062 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40616000 39664.062 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664576 40688.062 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761728 42736.062 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762288 42736.609 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956592 46832.609 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053744 48880.609 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73195 79170 19967 Total number of restraints before, now : 0 226554 make_re_422_> Number of previous, current restraints : 0 226554 make_re_423_> Number of previous, current selected restraints: 0 226554 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053744 48880.609 47.735 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 make_re_422_> Number of previous, current restraints : 226554 233848 make_re_423_> Number of previous, current selected restraints: 226554 233848 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053760 48880.625 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150912 50928.625 49.735 make_re_422_> Number of previous, current restraints : 233848 241156 make_re_423_> Number of previous, current selected restraints: 233848 233666 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150912 50928.625 49.735 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 : 241156 246798 make_re_423_> Number of previous, current selected restraints: 233666 239308 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150912 50928.625 49.735 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 : 246798 250886 make_re_423_> Number of previous, current selected restraints: 239308 243396 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150912 50928.625 49.735 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]: 56345216 55024.625 53.735 make_re_422_> Number of previous, current restraints : 250886 253042 make_re_423_> Number of previous, current selected restraints: 243396 245552 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345216 55024.625 53.735 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 : 253042 253907 make_re_423_> Number of previous, current selected restraints: 245552 246417 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892572 70207.594 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330224 71611.547 69.933 >> 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 : 253907 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 36 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 : 36.4468 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 0.017 0.017 0.79184 1.000 2 Bond angle potential : 14 0 0 2.443 2.443 1.9147 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.779 44.779 2.8231 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.298 1.298 0.89167E-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 : 36 0 2 0.543 0.543 29.540 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 1.782 1.782 0.74942E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 15.458 15.458 0.30479 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 123.612 123.612 2.2269 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 28.780 28.780 -1.6445 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 152 496 1510 3197 4239 4711 5777 7581 8900 9676 << 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 : 253907 54 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 : 4.4980 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 0.10989 1.000 2 Bond angle potential : 14 0 0 2.303 2.303 1.5277 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.984 44.984 2.7908 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.188 1.188 0.11050 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 0.362 0.362 -0.21863E-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 2.497 2.497 0.14715 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 115.457 115.457 0.92071E-01 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 136.072 136.072 0.82292 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 5.058 5.058 0.14128 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 29.454 29.454 -1.4383 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3196 4238 4711 5776 7577 8901 9674 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:50:44 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363848 22816.258 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57506 66427 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703984 23148.422 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 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 46475 57508 66429 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863288 23303.992 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62734 72466 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863344 23304.047 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997744 23435.297 22.886 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 50348 62736 72468 18720 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157060 23590.879 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67963 78505 18720 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565196 23989.449 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67965 78507 18721 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67965 78507 18721 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 54221 67965 78507 20161 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724512 24145.031 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73192 84544 20161 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724568 24145.086 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73194 84546 20162 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73194 84546 20162 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]: 31178112 30447.375 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284580 30551.348 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292772 30559.348 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309156 30575.348 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341924 30607.348 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374692 30639.348 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440228 30703.348 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440548 30703.660 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473316 30735.660 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538852 30799.660 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571620 30831.660 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702692 30959.660 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768228 31023.660 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899300 31151.660 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964836 31215.660 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32226980 31471.660 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358052 31599.660 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620196 31855.660 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751268 31983.660 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275556 32495.660 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537700 32751.660 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34061988 33263.660 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324132 33519.660 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372708 34543.660 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373108 34544.051 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897396 35056.051 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421684 35568.051 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470260 36592.051 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567412 38640.051 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40615988 39664.051 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664564 40688.051 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761716 42736.051 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762276 42736.598 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956580 46832.598 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053732 48880.598 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73194 79170 19966 Total number of restraints before, now : 0 226552 make_re_422_> Number of previous, current restraints : 0 226552 make_re_423_> Number of previous, current selected restraints: 0 226552 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053732 48880.598 47.735 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 make_re_422_> Number of previous, current restraints : 226552 233846 make_re_423_> Number of previous, current selected restraints: 226552 233846 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053748 48880.613 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150900 50928.613 49.735 make_re_422_> Number of previous, current restraints : 233846 241154 make_re_423_> Number of previous, current selected restraints: 233846 233664 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150900 50928.613 49.735 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 : 241154 246796 make_re_423_> Number of previous, current selected restraints: 233664 239306 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150900 50928.613 49.735 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 : 246796 250884 make_re_423_> Number of previous, current selected restraints: 239306 243394 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150900 50928.613 49.735 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]: 56345204 55024.613 53.735 make_re_422_> Number of previous, current restraints : 250884 253040 make_re_423_> Number of previous, current selected restraints: 243394 245550 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345204 55024.613 53.735 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 : 253040 253906 make_re_423_> Number of previous, current selected restraints: 245550 246416 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892560 70207.578 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330212 71611.531 69.933 >> 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 : 253906 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 29.3799 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 0.017 0.017 0.75713 1.000 2 Bond angle potential : 14 0 0 2.272 2.272 1.6546 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.188 44.188 2.7680 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.295 1.295 0.85795E-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 : 35 0 3 0.534 0.534 22.595 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 1.573 1.573 0.58374E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 16.135 16.135 0.32464 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 125.038 125.038 2.4541 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.000 0.000 0.10308 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 28.621 28.621 -1.6431 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 497 1510 3196 4239 4710 5775 7576 8901 9674 << 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 : 253906 54 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 : 7.9383 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 0.008 0.008 0.15013 1.000 2 Bond angle potential : 14 0 0 3.180 3.180 2.5376 1.000 3 Stereochemical cosine torsion poten: 18 0 0 43.019 43.019 2.6472 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.888 0.888 0.85879E-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 0.404 0.404 0.84217 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 2.606 2.606 0.16033 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 17.738 17.738 0.37821 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 122.185 122.185 1.1165 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 12.252 12.252 0.28931 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 110.596 110.596 1.0992 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 29.780 29.780 -1.3682 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3195 4236 4712 5775 7574 8902 9671 << 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 slars-bb 2.6.35-22-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): 2010/12/02 17:56:33 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363848 22816.258 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57506 66427 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703984 23148.422 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 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 46475 57508 66429 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863288 23303.992 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62734 72466 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863344 23304.047 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997744 23435.297 22.886 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 50348 62736 72468 18719 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157048 23590.867 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67962 78505 18719 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565184 23989.438 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67964 78507 18720 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67964 78507 18720 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 54221 67964 78507 20160 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724500 24145.020 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73191 84544 20160 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724556 24145.074 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73193 84546 20161 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73193 84546 20161 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]: 31178100 30447.363 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284568 30551.336 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292760 30559.336 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309144 30575.336 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341912 30607.336 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374680 30639.336 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440216 30703.336 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440536 30703.648 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473304 30735.648 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538840 30799.648 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571608 30831.648 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702680 30959.648 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768216 31023.648 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899288 31151.648 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964824 31215.648 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32226968 31471.648 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358040 31599.648 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620184 31855.648 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751256 31983.648 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275544 32495.648 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537688 32751.648 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34061976 33263.648 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324120 33519.648 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372696 34543.648 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373096 34544.039 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897384 35056.039 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421672 35568.039 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470248 36592.039 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567400 38640.039 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40615976 39664.039 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664552 40688.039 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761704 42736.039 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762264 42736.586 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956568 46832.586 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053720 48880.586 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73193 79170 19965 Total number of restraints before, now : 0 226550 make_re_422_> Number of previous, current restraints : 0 226550 make_re_423_> Number of previous, current selected restraints: 0 226550 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053720 48880.586 47.735 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 make_re_422_> Number of previous, current restraints : 226550 233844 make_re_423_> Number of previous, current selected restraints: 226550 233844 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053736 48880.602 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150888 50928.602 49.735 make_re_422_> Number of previous, current restraints : 233844 241152 make_re_423_> Number of previous, current selected restraints: 233844 233662 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150888 50928.602 49.735 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 : 241152 246794 make_re_423_> Number of previous, current selected restraints: 233662 239304 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150888 50928.602 49.735 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 : 246794 250882 make_re_423_> Number of previous, current selected restraints: 239304 243392 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150888 50928.602 49.735 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]: 56345192 55024.602 53.735 make_re_422_> Number of previous, current restraints : 250882 253038 make_re_423_> Number of previous, current selected restraints: 243392 245548 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345192 55024.602 53.735 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 : 253038 253905 make_re_423_> Number of previous, current selected restraints: 245548 246415 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892548 70207.562 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330200 71611.523 69.933 >> 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 : 253905 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 34 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 : 16.9406 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 0.017 0.017 0.86744 1.000 2 Bond angle potential : 14 0 0 2.290 2.290 1.6947 1.000 3 Stereochemical cosine torsion poten: 18 0 0 43.473 43.473 2.7135 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.294 1.294 0.86332E-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 : 34 0 2 0.498 0.498 9.7759 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 1.255 1.255 0.37205E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 17.119 17.119 0.35638 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 126.213 126.213 2.6501 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.10326 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.034 0.034 0.22266 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 28.251 28.251 -1.5668 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3195 4238 4713 5773 7573 8902 9671 << 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 : 253905 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 31 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 : 5.7656 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 0.12198 1.000 2 Bond angle potential : 14 0 0 2.721 2.721 1.8823 1.000 3 Stereochemical cosine torsion poten: 18 0 0 46.136 46.136 2.6436 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.241 1.241 0.16079 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 31 0 0 0.387 0.387 -0.12278 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 2.245 2.245 0.11892 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 2.862 2.862 0.14447 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 98.070 98.070 0.34502 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 76.485 76.485 1.4169 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 15.839 15.839 0.37061 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 29.756 29.756 -1.3161 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3194 4233 4714 5774 7572 8903 9669 << 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 slars-bb 2.6.35-22-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): 2010/12/02 18:02:22 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_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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 434 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]: 19292420 18840.254 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 3872 0 0 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19451696 18995.797 18.551 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 524 3855 3872 5226 6037 1439 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19610752 19151.125 18.702 patch_______> segment topology patched using RTF: 524 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 524 3856 3873 5228 6039 1440 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19664776 19203.883 18.754 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 7745 5228 6039 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19824080 19359.453 18.906 patch_______> segment topology patched using RTF: 525 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7711 7745 10454 12076 2879 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 19994776 19526.148 19.069 patch_______> segment topology patched using RTF: 1048 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 1048 7712 7746 10456 12078 2880 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20048800 19578.906 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 11618 10456 12078 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20208104 19734.477 19.272 patch_______> segment topology patched using RTF: 1049 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11567 11618 15682 18115 4319 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20353160 19876.133 19.410 patch_______> segment topology patched using RTF: 1572 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 1572 11568 11619 15684 18117 4320 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20407184 19928.891 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 15491 15684 18117 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20566488 20084.461 19.614 patch_______> segment topology patched using RTF: 1573 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15423 15491 20910 24154 5759 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20775344 20288.422 19.813 patch_______> segment topology patched using RTF: 2096 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 2096 15424 15492 20912 24156 5760 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20829368 20341.180 19.864 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 19364 20912 24156 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 20988672 20496.750 20.016 patch_______> segment topology patched using RTF: 2097 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19279 19364 26138 30193 7199 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21125408 20630.281 20.147 patch_______> segment topology patched using RTF: 2620 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 2620 19280 19365 26140 30195 7200 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21179432 20683.039 20.198 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 23237 26140 30195 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21338736 20838.609 20.350 patch_______> segment topology patched using RTF: 2621 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23135 23237 31366 36232 8639 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21502792 20998.820 20.507 patch_______> segment topology patched using RTF: 3144 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 3144 23136 23238 31368 36234 8640 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21567616 21062.125 20.568 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 27110 31368 36234 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21726920 21217.695 20.720 patch_______> segment topology patched using RTF: 3145 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26991 27110 36594 42271 10079 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 21923776 21409.938 20.908 patch_______> segment topology patched using RTF: 3668 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 3668 26992 27111 36596 42273 10080 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22001560 21485.898 20.982 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 30983 36596 42273 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22160864 21641.469 21.134 patch_______> segment topology patched using RTF: 3669 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30847 30983 41822 48310 11519 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22397080 21872.148 21.360 patch_______> segment topology patched using RTF: 4192 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 4192 30848 30984 41824 48312 11520 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22490424 21963.305 21.449 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 34856 41824 48312 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649728 22118.875 21.600 patch_______> segment topology patched using RTF: 4193 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34703 34856 47050 54349 12959 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22649784 22118.930 21.601 patch_______> segment topology patched using RTF: 4716 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 9 4716 34704 34857 47052 54351 12960 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 38729 47052 54351 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 22809088 22274.500 21.752 patch_______> segment topology patched using RTF: 4717 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38559 38729 52278 60388 14399 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23092544 22551.312 22.023 patch_______> segment topology patched using RTF: 5240 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 10 5240 38560 38730 52280 60390 14400 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23204544 22660.688 22.130 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 42602 52280 60390 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23363848 22816.258 22.282 patch_______> segment topology patched using RTF: 5241 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42415 42602 57506 66427 15839 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23703984 23148.422 22.606 patch_______> segment topology patched using RTF: 5764 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 11 5764 42416 42603 57508 66429 15840 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 46475 57508 66429 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863288 23303.992 22.758 patch_______> segment topology patched using RTF: 5765 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46271 46475 62734 72466 17279 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23863344 23304.047 22.758 patch_______> segment topology patched using RTF: 6288 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 12 6288 46272 46476 62736 72468 17280 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 23997744 23435.297 22.886 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 50348 62736 72468 18719 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24157048 23590.867 23.038 patch_______> segment topology patched using RTF: 6289 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50127 50348 67962 78505 18719 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24565184 23989.438 23.427 patch_______> segment topology patched using RTF: 6812 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67964 78507 18720 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 13 6812 50128 50349 67964 78507 18720 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 54221 67964 78507 20159 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724488 24145.008 23.579 patch_______> segment topology patched using RTF: 6813 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53983 54221 73190 84544 20159 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 24724544 24145.062 23.579 patch_______> segment topology patched using RTF: 7336 ; PRO ; CTER segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73192 84546 20160 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 14 7336 53984 54222 73192 84546 20160 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]: 31178088 30447.352 29.734 read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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.pdbLYS434.tmp wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984 openf___224_> Open 1XCK_protein.pdbLYS434.tmp read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. read_pd_403W> Treating residue type HID as a BLK (rigid body) even though topology information appears to be at least partially available. To treat this residue flexibly instead, remove the corresponding 'MODELLER BLK RESIDUE' REMARK from the input PDB file. 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]: 31284556 30551.324 29.835 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31292748 30559.324 29.843 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31309132 30575.324 29.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31341900 30607.324 29.890 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31374668 30639.324 29.921 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31440204 30703.324 29.984 generat_607W> Cannot find params in params file: CHARMM atoms : C UNDF IUPAC atoms : C N Atom indices : 2946 2948 Residues : LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 31440524 30703.637 29.984 addprm__440W> Adding params (mean,force,period): 1.3284 300.0000 0 For atoms: C UNDF Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31473292 30735.637 30.015 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31538828 30799.637 30.078 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31571596 30831.637 30.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31702668 30959.637 30.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31768204 31023.637 30.297 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31899276 31151.637 30.422 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 31964812 31215.637 30.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32226956 31471.637 30.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32358028 31599.637 30.859 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32620172 31855.637 31.109 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 32751244 31983.637 31.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33275532 32495.637 31.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 33537676 32751.637 31.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34061964 33263.637 32.484 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 34324108 33519.637 32.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35372684 34543.637 33.734 generat_607W> Cannot find params in params file: CHARMM atoms : CT1 C UNDF IUPAC atoms : CA C N Atom indices : 2941 2946 2948 Residues : LEU LEU HID Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 35373084 34544.027 33.734 addprm__440W> Adding params (mean,force,period): 116.1717 60.0000 0 For atoms: CT1 C UNDF generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C O IUPAC atoms : N C O Atom indices : 2948 2946 2947 Residues : HID LEU LEU addprm__440W> Adding params (mean,force,period): 122.9521 60.0000 0 For atoms: UNDF C O Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 35897372 35056.027 34.234 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 36421660 35568.027 34.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 37470236 36592.027 35.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 39567388 38640.027 37.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 40615964 39664.027 38.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 41664540 40688.027 39.734 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 43761692 42736.027 41.734 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 CT2 IUPAC atoms : N C CA CB Atom indices : 2948 2946 2941 2942 Residues : HID LEU LEU LEU Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 43762252 42736.574 41.735 addprm__440W> Adding params (mean,force,period): 73.6813 10.0000 3 For atoms: UNDF C CT1 CT2 generat_607W> Cannot find params in params file: CHARMM atoms : UNDF C CT1 NH1 IUPAC atoms : N C CA N Atom indices : 2948 2946 2941 2940 Residues : HID LEU LEU LEU addprm__440W> Adding params (mean,force,period): -48.1764 10.0000 3 For atoms: UNDF C CT1 NH1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 47956556 46832.574 45.735 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 50053708 48880.574 47.735 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 54222 73192 79170 19964 Total number of restraints before, now : 0 226548 make_re_422_> Number of previous, current restraints : 0 226548 make_re_423_> Number of previous, current selected restraints: 0 226548 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053708 48880.574 47.735 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 make_re_422_> Number of previous, current restraints : 226548 233842 make_re_423_> Number of previous, current selected restraints: 226548 233842 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 50053724 48880.590 47.735 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: 7490 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 52150876 50928.590 49.735 make_re_422_> Number of previous, current restraints : 233842 241150 make_re_423_> Number of previous, current selected restraints: 233842 233660 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150876 50928.590 49.735 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 : 241150 246792 make_re_423_> Number of previous, current selected restraints: 233660 239302 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150876 50928.590 49.735 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 : 246792 250880 make_re_423_> Number of previous, current selected restraints: 239302 243390 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 52150876 50928.590 49.735 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]: 56345180 55024.590 53.735 make_re_422_> Number of previous, current restraints : 250880 253036 make_re_423_> Number of previous, current selected restraints: 243390 245546 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 56345180 55024.590 53.735 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 : 253036 253904 make_re_423_> Number of previous, current selected restraints: 245546 246414 pick_re_612_> Number of MODEL atoms, selected restraints; 9 54 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 71892536 70207.555 68.562 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 73330188 71611.516 69.933 >> 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 : 253904 54 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 35 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 : 9.7446 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 0.015 0.015 0.64337 1.000 2 Bond angle potential : 14 0 0 2.196 2.196 1.5516 1.000 3 Stereochemical cosine torsion poten: 18 0 0 44.113 44.113 2.8011 1.000 4 Stereochemical improper torsion pot: 3 0 0 1.363 1.363 0.96802E-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 : 35 0 0 0.414 0.414 2.6935 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 1.869 1.869 0.82424E-01 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 17.551 17.551 0.37147 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 1 126.969 126.969 2.7800 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 0.028 0.028 0.94805E-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 28.990 28.990 -1.5866 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3194 4233 4713 5772 7572 8903 9668 << 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 : 253904 54 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 : 6.1209 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 0.10711 1.000 2 Bond angle potential : 14 0 0 2.523 2.523 1.6424 1.000 3 Stereochemical cosine torsion poten: 18 0 0 47.927 47.927 2.8280 1.000 4 Stereochemical improper torsion pot: 3 0 0 0.814 0.814 0.72591E-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 : 27 0 0 0.385 0.385 -0.15571 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 2.504 2.504 0.14803 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 15.814 15.814 0.31503 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 93.528 93.528 0.41153 1.000 16 Sidechain Chi_3 dihedral restraints: 1 0 0 85.225 85.225 1.2419 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 117.951 117.951 0.95231 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 29.736 29.736 -1.4423 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: 2950 2958 1.328 serious non-bonded atom clash: 2951 2958 2.245 serious non-bonded atom clash: 5305 5312 2.240 serious non-bonded atom clash: 5312 5325 2.276 serious non-bonded atom clash: 6806 6814 1.330 serious non-bonded atom clash: 6807 6814 2.258 serious non-bonded atom clash: 1066210670 1.328 serious non-bonded atom clash: 1066310670 2.246 serious non-bonded atom clash: 1301713024 2.281 serious non-bonded atom clash: 1451814526 1.333 serious non-bonded atom clash: 1451914526 2.257 serious non-bonded atom clash: 1687316880 2.277 serious non-bonded atom clash: 1837418382 1.330 serious non-bonded atom clash: 1837518382 2.257 serious non-bonded atom clash: 2223022238 1.334 serious non-bonded atom clash: 2223122238 2.260 serious non-bonded atom clash: 2458524592 2.259 serious non-bonded atom clash: 2608626094 1.328 serious non-bonded atom clash: 2608726094 2.251 serious non-bonded atom clash: 2994229950 1.330 serious non-bonded atom clash: 2994329950 2.254 serious non-bonded atom clash: 3379833806 1.325 serious non-bonded atom clash: 3379933806 2.249 serious non-bonded atom clash: 3765437662 1.329 serious non-bonded atom clash: 3765537662 2.253 serious non-bonded atom clash: 4000940016 2.266 serious non-bonded atom clash: 4151041518 1.326 serious non-bonded atom clash: 4151141518 2.249 serious non-bonded atom clash: 4536645374 1.330 serious non-bonded atom clash: 4536745374 2.256 serious non-bonded atom clash: 4922249230 1.324 serious non-bonded atom clash: 4922349230 2.238 serious non-bonded atom clash: 5157751584 2.298 serious non-bonded atom clash: 5307853086 1.329 serious non-bonded atom clash: 5307953086 2.251 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: 14 0 22 29 88 151 496 1509 3193 4230 4716 5773 7567 8905 9665 << end of ENERGY. openf___224_> Open 1XCK_protein.pdb wrpdb___568_> Residues, atoms, selected atoms: 7336 53984 53984