MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2019/05/05 20:45:45 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open bak_blast5.pir Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265439 259.218 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266889 260.634 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269789 263.466 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 275589 269.130 0.263 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 278629 272.099 0.266 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 395313 386.048 0.377 check_prot_W> Alignment sequence domain1 protein type '' does not contain 'sequence' or 'structure'; it will be treated as a sequence without structure Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 396165 386.880 0.378 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 397033 387.728 0.379 Read the alignment from file : bak_blast5.pir Total number of alignment positions: 218 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 3UK8A 214 1 3UK8A 2 domain1 218 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ./3UK8A.atm Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 462958 452.107 0.442 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 462958 452.107 0.442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463129 452.274 0.442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 463979 453.104 0.442 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 465237 454.333 0.444 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 467141 456.192 0.446 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 467141 456.192 0.446 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 467231 456.280 0.446 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 470087 459.069 0.448 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 470087 459.069 0.448 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 470222 459.201 0.448 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 474506 463.385 0.453 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 474506 463.385 0.453 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 474704 463.578 0.453 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481130 469.854 0.459 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481130 469.854 0.459 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481427 470.144 0.459 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 491049 479.540 0.468 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 491049 479.540 0.468 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 491499 479.979 0.469 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 505949 494.091 0.483 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 505949 494.091 0.483 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506624 494.750 0.483 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 528282 515.900 0.504 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 528183 515.804 0.504 check_ali___> Checking the sequence-structure alignment. Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 667435 651.792 0.637 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 669035 653.354 0.638 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 673015 657.241 0.642 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 675015 659.194 0.644 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 678015 662.124 0.647 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 682515 666.519 0.651 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 688087 671.960 0.656 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 690887 674.694 0.659 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 695087 678.796 0.663 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 701387 684.948 0.669 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 704159 687.655 0.672 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 705559 689.022 0.673 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 739628 722.293 0.705 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 901132 880.012 0.859 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 925100 903.418 0.882 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 218 1629 1662 0 0 667 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 994816 971.500 0.949 patch_______> segment topology patched using RTF: 1 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 1 218 1629 1662 2252 2670 667 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1071592 1046.477 1.022 patch_______> segment topology patched using RTF: 218 ; ALA ; CTER segments residues atoms bonds angles dihedrals impropers: 1 218 1630 1663 2254 2672 668 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 218 1630 1663 2254 2672 668 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: 1497 133 openf___224_> Open domain1.ini wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1178621 1150.997 1.124 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1186813 1158.997 1.132 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1203197 1174.997 1.147 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1235965 1206.997 1.179 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1268733 1238.997 1.210 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1334269 1302.997 1.272 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1367037 1334.997 1.304 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1399805 1366.997 1.335 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1465341 1430.997 1.397 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1596413 1558.997 1.522 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1661949 1622.997 1.585 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1663 2254 2561 657 Total number of restraints before, now : 0 7135 make_re_422_> Number of previous, current restraints : 0 7135 make_re_423_> Number of previous, current selected restraints: 0 7135 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1784186 1742.369 1.702 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1849738 1806.385 1.764 make_re_422_> Number of previous, current restraints : 7135 7351 make_re_423_> Number of previous, current selected restraints: 7135 7351 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1849738 1806.385 1.764 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 228 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 7351 7568 make_re_423_> Number of previous, current selected restraints: 7351 7340 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1849738 1806.385 1.764 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7568 7740 make_re_423_> Number of previous, current selected restraints: 7340 7512 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1849738 1806.385 1.764 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7740 7865 make_re_423_> Number of previous, current selected restraints: 7512 7637 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1849738 1806.385 1.764 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1980810 1934.385 1.889 make_re_422_> Number of previous, current restraints : 7865 7922 make_re_423_> Number of previous, current selected restraints: 7637 7694 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1980810 1934.385 1.889 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi4.mdt mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 3UK8A getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 7922 7943 make_re_423_> Number of previous, current selected restraints: 7694 7715 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 2450214 2392.787 2.337 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2581286 2520.787 2.462 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2843430 2776.787 2.712 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2974502 2904.787 2.837 make_re_422_> Number of previous, current restraints : 7943 12613 make_re_423_> Number of previous, current selected restraints: 7715 12385 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3236646 3160.787 3.087 make_re_422_> Number of previous, current restraints : 12613 17243 make_re_423_> Number of previous, current selected restraints: 12385 17015 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3760934 3672.787 3.587 make_re_422_> Number of previous, current restraints : 17243 20188 make_re_423_> Number of previous, current selected restraints: 17015 19960 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 20188 21965 make_re_423_> Number of previous, current selected restraints: 19960 21737 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 21965 21965 make_re_423_> Number of previous, current selected restraints: 21737 21737 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 21965 21965 make_re_423_> Number of previous, current selected restraints: 21737 21737 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 21965 21965 make_re_423_> Number of previous, current selected restraints: 21737 21737 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 21965 21965 make_re_423_> Number of previous, current selected restraints: 21737 21737 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 21965 21965 make_re_423_> Number of previous, current selected restraints: 21737 21737 rmdupl__427_> 1302 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 21965 20435 openf___224_> Open domain1.rsr openf___224_> Open domain1.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3897682 3806.330 3.717 rdcsr2__307_> Number of restraints read : 20435 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 20435 20435 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 3897702 3806.350 3.717 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4229406 4130.279 4.033 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 151.1094 4 4 iupac_m_487_> NH1/2 swapped: -174.4024 22 22 iupac_m_486_> OE1/2 will be swapped: -149.9145 25 25 iupac_m_487_> NH1/2 swapped: -176.9388 53 53 iupac_m_485_> OD1/2 will be swapped: 167.3862 82 82 iupac_m_486_> OE1/2 will be swapped: -176.0207 86 86 iupac_m_487_> NH1/2 swapped: 178.4611 115 115 iupac_m_485_> OD1/2 will be swapped: 137.8597 176 176 iupac_m_487_> NH1/2 swapped: 179.2082 178 178 iupac_m_487_> NH1/2 swapped: -179.2025 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3576 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1134.4315 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 : 1663 0 0 0.005 0.005 13.879 1.000 2 Bond angle potential : 2254 1 6 2.180 2.180 213.40 1.000 3 Stereochemical cosine torsion poten: 1031 0 37 48.272 48.272 374.03 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.188 1.188 22.816 1.000 5 Soft-sphere overlap restraints : 3576 0 0 0.002 0.002 1.2437 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 6 0.119 0.119 80.164 1.000 10 Distance restraints 2 (N-O) : 4630 2 7 0.166 0.166 146.88 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: 217 1 3 4.203 4.203 45.206 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 1 48.979 48.979 4.4134 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 52.421 52.421 29.406 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 53.427 53.427 28.005 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 67.599 67.599 11.749 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) : 2945 0 0 0.290 0.290 46.445 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: 216 7 19 24.914 38.836 44.434 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 2 0.511 0.511 72.358 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990001 # Heavy relative violation of each residue is written to: domain1.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16504.7383 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1713 6S 6S N CA 37 38 131.46 107.00 24.46 7.03 107.00 24.46 7.03 ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -69.38 -70.20 16.62 1.22 -62.90 162.34 21.44 1 2K 2K N CA 5 6 156.99 140.40 -40.80 2 5607 2K 3D C N 12 14 -58.14 -70.90 24.87 0.84 -63.30 169.03 21.18 2 3D 3D N CA 14 15 128.95 150.30 -40.00 3 5609 4D 5T C N 28 30 -174.20 -124.80 50.15 2.42 -63.20 -160.56 32.57 3 5T 5T N CA 30 31 152.20 143.50 -42.10 4 5610 5T 6S C N 35 37 71.99 56.90 16.23 1.52 -72.40 -170.99 9.28 4 6S 6S N CA 37 38 30.43 36.40 152.40 5 5711 106A 107D C N 765 767 75.83 -70.90 163.79 13.74 -70.90 163.79 13.74 5 107D 107D N CA 767 768 -136.91 150.30 150.30 6 5770 165V 166E C N 1221 1223 -59.11 -63.60 8.30 0.96 -69.30 170.52 13.37 6 166E 166E N CA 1223 1224 -47.29 -40.30 142.50 7 5771 166E 167N C N 1230 1232 -117.07 -119.90 96.44 4.32 55.90 172.97 19.39 7 167N 167N N CA 1232 1233 40.60 137.00 39.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 12 19 82 97 144 160 196 240 266 306 << end of ENERGY. openf___224_> Open domain1.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: -140.1164 3 3 iupac_m_485_> OD1/2 will be swapped: 165.5401 4 4 iupac_m_486_> OE1/2 will be swapped: -101.9626 40 40 iupac_m_487_> NH1/2 swapped: 169.6956 53 53 iupac_m_487_> NH1/2 swapped: -178.3697 76 76 iupac_m_487_> NH1/2 swapped: 178.8455 115 115 iupac_m_486_> OE1/2 will be swapped: 168.6931 121 121 iupac_m_487_> NH1/2 swapped: 172.3561 129 129 iupac_m_486_> OE1/2 will be swapped: 136.8739 131 131 iupac_m_486_> OE1/2 will be swapped: 118.9210 157 157 iupac_m_486_> OE1/2 will be swapped: -172.3739 166 166 iupac_m_486_> OE1/2 will be swapped: -174.2319 174 174 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3593 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1059.2306 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 : 1663 0 0 0.006 0.006 14.268 1.000 2 Bond angle potential : 2254 0 3 2.080 2.080 189.91 1.000 3 Stereochemical cosine torsion poten: 1031 0 37 47.831 47.831 367.03 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.345 1.345 27.358 1.000 5 Soft-sphere overlap restraints : 3593 0 0 0.002 0.002 1.0134 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.089 0.089 47.761 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.131 0.131 97.366 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: 217 0 1 3.586 3.586 32.910 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 1 60.145 60.145 21.835 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 48.632 48.632 36.610 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 1 63.607 63.607 39.588 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 102.696 102.696 12.894 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) : 2945 0 0 0.295 0.295 50.748 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: 216 4 18 24.347 29.764 31.235 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 1 0.565 0.565 88.710 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990002 # Heavy relative violation of each residue is written to: domain1.V99990002 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 17410.9062 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -107.29 -118.00 45.04 2.30 -62.90 143.40 21.26 1 2K 2K N CA 5 6 -177.15 139.10 -40.80 2 5608 3D 4D C N 20 22 -62.61 -70.90 31.99 1.21 -63.30 159.40 19.72 2 4D 4D N CA 22 23 119.40 150.30 -40.00 3 5609 4D 5T C N 28 30 -86.40 -78.10 70.73 2.76 -63.20 100.57 14.44 3 5T 5T N CA 30 31 -139.96 149.80 -42.10 4 5711 106A 107D C N 765 767 74.71 -63.30 165.42 20.46 -70.90 165.42 13.88 4 107D 107D N CA 767 768 -131.20 -40.00 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 4 24 68 95 167 162 189 241 286 295 << end of ENERGY. openf___224_> Open domain1.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 172.6514 3 3 iupac_m_485_> OD1/2 will be swapped: -94.5567 14 14 iupac_m_486_> OE1/2 will be swapped: 175.5132 25 25 iupac_m_486_> OE1/2 will be swapped: -177.9500 27 27 iupac_m_485_> OD1/2 will be swapped: 113.3449 37 37 iupac_m_486_> OE1/2 will be swapped: 126.2599 40 40 iupac_m_487_> NH1/2 swapped: -178.6654 53 53 iupac_m_487_> NH1/2 swapped: -177.0415 59 59 iupac_m_486_> OE1/2 will be swapped: 167.6639 166 166 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3643 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 930.8997 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 : 1663 0 0 0.005 0.005 11.925 1.000 2 Bond angle potential : 2254 0 3 1.957 1.957 169.87 1.000 3 Stereochemical cosine torsion poten: 1031 0 34 47.763 47.763 366.13 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.128 1.128 20.640 1.000 5 Soft-sphere overlap restraints : 3643 0 0 0.001 0.001 0.91212 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.078 0.078 35.794 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.121 0.121 83.861 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: 217 0 0 3.531 3.531 31.910 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 58.835 58.835 4.1995 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 1 50.858 50.858 27.816 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 1 53.914 53.914 31.008 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 103.348 103.348 14.595 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) : 2945 0 0 0.288 0.288 49.877 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: 216 5 14 23.817 33.098 29.723 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 1 0.437 0.437 52.648 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990003 # Heavy relative violation of each residue is written to: domain1.V99990003 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16078.8018 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -71.86 -70.20 3.19 0.26 -62.90 178.70 22.73 1 2K 2K N CA 5 6 137.68 140.40 -40.80 2 5607 2K 3D C N 12 14 -124.41 -96.50 28.41 1.16 -63.30 160.94 17.21 2 3D 3D N CA 14 15 108.89 114.20 -40.00 3 5608 3D 4D C N 20 22 -92.76 -70.90 39.93 1.36 -63.30 139.44 19.10 3 4D 4D N CA 22 23 -176.29 150.30 -40.00 4 5609 4D 5T C N 28 30 -79.78 -78.10 11.59 0.44 -63.20 157.50 21.30 4 5T 5T N CA 30 31 161.27 149.80 -42.10 5 5711 106A 107D C N 765 767 75.98 -70.90 163.17 13.69 -70.90 163.17 13.69 5 107D 107D N CA 767 768 -138.62 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 5 22 67 90 160 158 204 230 279 340 << end of ENERGY. openf___224_> Open domain1.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 165.9011 37 37 iupac_m_486_> OE1/2 will be swapped: 130.9528 40 40 iupac_m_487_> NH1/2 swapped: -174.5575 76 76 iupac_m_485_> OD1/2 will be swapped: 149.8006 82 82 iupac_m_486_> OE1/2 will be swapped: 179.9344 121 121 iupac_m_487_> NH1/2 swapped: -175.8692 129 129 iupac_m_487_> NH1/2 swapped: 179.6625 178 178 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3673 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 905.6903 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 : 1663 0 0 0.005 0.005 11.998 1.000 2 Bond angle potential : 2254 0 2 1.957 1.957 169.59 1.000 3 Stereochemical cosine torsion poten: 1031 0 31 47.753 47.753 366.99 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.034 1.034 18.375 1.000 5 Soft-sphere overlap restraints : 3673 0 0 0.001 0.001 0.66395 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.081 0.081 38.729 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.119 0.119 81.942 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: 217 0 1 3.564 3.564 32.508 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 46.657 46.657 -7.1767 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 50.991 50.991 29.642 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 60.741 60.741 31.892 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 102.115 102.115 13.408 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) : 2945 0 0 0.286 0.286 48.360 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: 216 5 13 23.551 35.071 22.204 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 0 0.413 0.413 46.557 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990004 # Heavy relative violation of each residue is written to: domain1.V99990004 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 15502.9277 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -95.54 -118.00 22.91 0.95 -62.90 178.58 25.09 1 2K 2K N CA 5 6 143.63 139.10 -40.80 2 5607 2K 3D C N 12 14 -70.64 -70.90 13.11 0.63 -63.30 177.34 21.46 2 3D 3D N CA 14 15 137.19 150.30 -40.00 3 5608 3D 4D C N 20 22 -86.24 -70.90 15.70 1.28 -63.30 174.54 22.99 3 4D 4D N CA 22 23 146.98 150.30 -40.00 4 5609 4D 5T C N 28 30 -150.69 -124.80 25.97 1.42 -63.20 -163.00 30.95 4 5T 5T N CA 30 31 141.39 143.50 -42.10 5 5711 106A 107D C N 765 767 75.79 -70.90 163.24 13.70 -70.90 163.24 13.70 5 107D 107D N CA 767 768 -138.07 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 3 26 62 101 150 168 214 224 290 300 << end of ENERGY. openf___224_> Open domain1.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 161.7011 3 3 iupac_m_487_> NH1/2 swapped: 175.7039 22 22 iupac_m_486_> OE1/2 will be swapped: -135.6130 25 25 iupac_m_486_> OE1/2 will be swapped: 132.8688 27 27 iupac_m_487_> NH1/2 swapped: 177.4090 53 53 iupac_m_486_> OE1/2 will be swapped: 151.0696 86 86 iupac_m_487_> NH1/2 swapped: 176.4920 115 115 iupac_m_487_> NH1/2 swapped: -179.3676 129 129 iupac_m_485_> OD1/2 will be swapped: 114.2990 133 133 iupac_m_486_> OE1/2 will be swapped: 96.9867 171 171 iupac_m_487_> NH1/2 swapped: 179.2509 178 178 iupac_m_487_> NH1/2 swapped: -178.7381 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3643 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 999.6869 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 : 1663 0 0 0.005 0.005 12.972 1.000 2 Bond angle potential : 2254 0 2 1.993 1.993 175.81 1.000 3 Stereochemical cosine torsion poten: 1031 0 39 48.238 48.238 373.64 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.098 1.098 19.815 1.000 5 Soft-sphere overlap restraints : 3643 0 0 0.001 0.001 0.95130 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.087 0.087 44.497 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.120 0.120 83.596 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: 217 0 1 3.522 3.522 31.741 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 53.993 53.993 6.8769 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 56.576 56.576 40.843 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 59.725 59.725 30.391 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 86.181 86.181 11.311 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) : 2945 0 0 0.315 0.315 59.782 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: 216 4 13 23.398 31.075 23.682 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 0 0.558 0.558 83.779 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990005 # Heavy relative violation of each residue is written to: domain1.V99990005 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16637.4609 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -101.70 -118.00 28.95 1.11 -62.90 160.73 19.10 1 2K 2K N CA 5 6 115.17 139.10 -40.80 2 5607 2K 3D C N 12 14 50.99 54.50 3.53 0.39 -63.30 140.27 23.83 2 3D 3D N CA 14 15 41.32 40.90 -40.00 3 5609 4D 5T C N 28 30 -114.60 -124.80 12.01 0.73 -63.20 175.75 25.96 3 5T 5T N CA 30 31 149.84 143.50 -42.10 4 5711 106A 107D C N 765 767 76.19 -70.90 163.32 13.70 -70.90 163.32 13.70 4 107D 107D N CA 767 768 -138.72 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 5 26 84 101 142 156 202 242 283 295 << end of ENERGY. openf___224_> Open domain1.B99990005.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_486_> OE1/2 will be swapped: -162.6218 25 25 iupac_m_487_> NH1/2 swapped: 178.9989 53 53 iupac_m_487_> NH1/2 swapped: 174.4475 129 129 iupac_m_486_> OE1/2 will be swapped: 179.7815 143 143 iupac_m_486_> OE1/2 will be swapped: 117.5890 157 157 iupac_m_486_> OE1/2 will be swapped: 99.5672 171 171 iupac_m_487_> NH1/2 swapped: -179.8220 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3618 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1033.2236 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 : 1663 0 0 0.005 0.005 12.520 1.000 2 Bond angle potential : 2254 0 2 2.002 2.002 179.35 1.000 3 Stereochemical cosine torsion poten: 1031 0 34 47.716 47.716 368.23 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.152 1.152 21.656 1.000 5 Soft-sphere overlap restraints : 3618 0 0 0.001 0.001 0.73952 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.081 0.081 38.534 1.000 10 Distance restraints 2 (N-O) : 4630 2 7 0.157 0.157 134.19 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: 217 0 2 3.618 3.618 33.504 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 56.717 56.717 6.4525 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 1 45.505 45.505 25.298 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 58.296 58.296 29.877 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 102.839 102.839 13.338 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) : 2945 0 1 0.298 0.298 52.952 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: 216 7 15 24.382 37.143 36.005 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 0 0.535 0.535 80.576 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990006 # Heavy relative violation of each residue is written to: domain1.V99990006 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16594.2168 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -104.18 -118.00 21.08 1.07 -62.90 169.29 24.42 1 2K 2K N CA 5 6 155.02 139.10 -40.80 2 5607 2K 3D C N 12 14 -74.93 -70.90 21.31 0.86 -63.30 149.23 19.14 2 3D 3D N CA 14 15 171.22 150.30 -40.00 3 5608 3D 4D C N 20 22 -69.24 -96.50 32.00 1.33 -63.30 137.56 16.63 3 4D 4D N CA 22 23 97.43 114.20 -40.00 4 5609 4D 5T C N 28 30 -142.98 -124.80 18.31 1.02 -63.20 -166.21 30.07 4 5T 5T N CA 30 31 141.30 143.50 -42.10 5 5711 106A 107D C N 765 767 76.39 -70.90 163.30 13.70 -70.90 163.30 13.70 5 107D 107D N CA 767 768 -139.19 150.30 150.30 6 5770 165V 166E C N 1221 1223 -57.01 -63.60 12.53 1.45 -69.30 166.99 13.17 6 166E 166E N CA 1223 1224 -50.96 -40.30 142.50 7 5771 166E 167N C N 1230 1232 -119.07 -119.90 92.17 4.17 55.90 175.05 19.42 7 167N 167N N CA 1232 1233 44.83 137.00 39.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 7 20 84 103 152 161 187 253 259 301 << end of ENERGY. openf___224_> Open domain1.B99990006.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 143.4070 3 3 iupac_m_485_> OD1/2 will be swapped: 132.0366 4 4 iupac_m_486_> OE1/2 will be swapped: -176.3391 25 25 iupac_m_486_> OE1/2 will be swapped: -172.0212 40 40 iupac_m_485_> OD1/2 will be swapped: 111.4119 56 56 iupac_m_487_> NH1/2 swapped: -178.3433 59 59 iupac_m_486_> OE1/2 will be swapped: 159.5507 86 86 iupac_m_485_> OD1/2 will be swapped: 134.4605 103 103 iupac_m_485_> OD1/2 will be swapped: 129.8230 107 107 iupac_m_487_> NH1/2 swapped: -179.7702 115 115 iupac_m_485_> OD1/2 will be swapped: 121.4832 123 123 iupac_m_487_> NH1/2 swapped: -179.9344 178 178 iupac_m_487_> NH1/2 swapped: -179.7973 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3595 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 934.1049 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 : 1663 0 0 0.005 0.005 11.651 1.000 2 Bond angle potential : 2254 0 3 1.945 1.945 168.36 1.000 3 Stereochemical cosine torsion poten: 1031 0 32 47.888 47.888 367.52 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.124 1.124 20.354 1.000 5 Soft-sphere overlap restraints : 3595 0 0 0.001 0.001 0.75818 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.078 0.078 35.658 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.119 0.119 81.238 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: 217 0 0 3.471 3.471 30.836 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 52.777 52.777 9.1272 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 46.328 46.328 28.883 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 63.085 63.085 32.187 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 100.872 100.872 13.947 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) : 2945 0 0 0.277 0.277 43.975 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: 216 4 13 23.637 31.747 27.008 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 1 0.473 0.473 62.605 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990007 # Heavy relative violation of each residue is written to: domain1.V99990007 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 15770.4775 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5607 2K 3D C N 12 14 -80.27 -70.90 15.66 0.56 -63.30 158.08 20.57 1 3D 3D N CA 14 15 162.84 150.30 -40.00 2 5608 3D 4D C N 20 22 -98.06 -96.50 18.93 0.80 -63.30 176.52 19.93 2 4D 4D N CA 22 23 133.07 114.20 -40.00 3 5609 4D 5T C N 28 30 -110.22 -124.80 20.57 1.23 -63.20 166.66 24.50 3 5T 5T N CA 30 31 158.01 143.50 -42.10 4 5711 106A 107D C N 765 767 76.86 -70.90 163.72 13.73 -70.90 163.72 13.73 4 107D 107D N CA 767 768 -139.17 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 9 18 78 93 152 152 196 244 286 324 << end of ENERGY. openf___224_> Open domain1.B99990007.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_486_> OE1/2 will be swapped: 178.0634 27 27 iupac_m_485_> OD1/2 will be swapped: 168.0794 37 37 iupac_m_487_> NH1/2 swapped: 172.8526 53 53 iupac_m_487_> NH1/2 swapped: -179.0896 59 59 iupac_m_486_> OE1/2 will be swapped: 170.8979 86 86 iupac_m_483_> CD1/2 CE1/2 swapped: -108.6207 113 113 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: -169.4756 115 115 iupac_m_487_> NH1/2 swapped: -179.7175 129 129 iupac_m_486_> OE1/2 will be swapped: 92.6001 131 131 iupac_m_487_> NH1/2 swapped: -177.5665 178 178 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3612 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1022.2306 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 : 1663 0 0 0.005 0.005 12.845 1.000 2 Bond angle potential : 2254 0 3 2.020 2.020 179.70 1.000 3 Stereochemical cosine torsion poten: 1031 0 29 47.746 47.746 368.45 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.219 1.219 22.921 1.000 5 Soft-sphere overlap restraints : 3612 0 0 0.001 0.001 0.79476 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.082 0.082 40.163 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.120 0.120 84.644 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: 217 0 1 3.510 3.510 31.524 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 59.711 59.711 16.328 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 3 50.684 50.684 42.390 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 65.246 65.246 32.713 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 71.640 71.640 9.9452 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) : 2945 0 0 0.317 0.317 60.257 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: 216 4 15 23.422 32.435 22.081 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 1 0.594 0.594 97.478 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990008 # Heavy relative violation of each residue is written to: domain1.V99990008 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16736.9453 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -73.60 -70.20 4.87 0.29 -62.90 175.64 23.41 1 2K 2K N CA 5 6 143.88 140.40 -40.80 2 5607 2K 3D C N 12 14 -74.23 -70.90 4.67 0.38 -63.30 173.32 22.07 2 3D 3D N CA 14 15 147.02 150.30 -40.00 3 5609 4D 5T C N 28 30 -107.50 -124.80 18.35 0.80 -63.20 -175.13 21.08 3 5T 5T N CA 30 31 137.39 143.50 -42.10 4 5711 106A 107D C N 765 767 73.70 -70.90 161.23 13.53 -70.90 161.23 13.53 4 107D 107D N CA 767 768 -138.38 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 9 25 75 90 159 171 210 238 266 305 << end of ENERGY. openf___224_> Open domain1.B99990008.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: 176.7854 3 3 iupac_m_486_> OE1/2 will be swapped: -166.5249 27 27 iupac_m_487_> NH1/2 swapped: -176.4496 53 53 iupac_m_487_> NH1/2 swapped: -179.5813 59 59 iupac_m_486_> OE1/2 will be swapped: 97.4398 86 86 iupac_m_487_> NH1/2 swapped: 178.6958 115 115 iupac_m_486_> OE1/2 will be swapped: -149.8620 121 121 iupac_m_486_> OE1/2 will be swapped: 146.9193 149 149 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3500 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 927.8887 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 : 1663 0 0 0.005 0.005 11.563 1.000 2 Bond angle potential : 2254 0 2 1.950 1.950 168.64 1.000 3 Stereochemical cosine torsion poten: 1031 0 35 47.955 47.955 365.77 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.153 1.153 21.472 1.000 5 Soft-sphere overlap restraints : 3500 0 0 0.001 0.001 0.62354 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.077 0.077 34.949 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.119 0.119 81.902 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: 217 0 0 3.447 3.447 30.414 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 54.220 54.220 6.0257 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 0 42.628 42.628 21.437 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 58.354 58.354 31.948 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 96.049 96.049 15.370 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) : 2945 0 0 0.282 0.282 46.158 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: 216 5 14 24.042 31.942 34.165 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 0 0.457 0.457 57.458 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990009 # Heavy relative violation of each residue is written to: domain1.V99990009 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 15719.4785 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -84.12 -70.20 31.69 1.98 -62.90 151.82 20.94 1 2K 2K N CA 5 6 168.87 140.40 -40.80 2 5607 2K 3D C N 12 14 -72.50 -70.90 32.29 1.51 -63.30 137.76 17.57 2 3D 3D N CA 14 15 -177.45 150.30 -40.00 3 5608 3D 4D C N 20 22 -76.70 -96.50 41.40 1.74 -63.30 118.60 13.88 3 4D 4D N CA 22 23 77.85 114.20 -40.00 4 5609 4D 5T C N 28 30 -105.03 -124.80 21.36 1.27 -63.20 171.50 24.78 4 5T 5T N CA 30 31 151.58 143.50 -42.10 5 5711 106A 107D C N 765 767 75.83 -70.90 163.38 13.71 -70.90 163.38 13.71 5 107D 107D N CA 767 768 -137.85 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 3 25 69 87 147 167 185 230 280 288 << end of ENERGY. openf___224_> Open domain1.B99990009.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 openf___224_> Open domain1.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4229426 4130.299 4.033 read_mo_297_> Segments, residues, atoms: 1 218 1630 read_mo_298_> Segment: 1 1 218 1630 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1630 1630 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 1630 10164 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 11383 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 12139 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 13006 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14226 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 14768 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 16201 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 17380 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 18703 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20391 pick_re_612_> Number of MODEL atoms, selected restraints; 1630 20435 iupac_m_485_> OD1/2 will be swapped: -145.7417 14 14 iupac_m_487_> NH1/2 swapped: 178.7780 22 22 iupac_m_486_> OE1/2 will be swapped: -122.1577 25 25 iupac_m_485_> OD1/2 will be swapped: 155.4769 37 37 iupac_m_487_> NH1/2 swapped: -176.0104 53 53 iupac_m_487_> NH1/2 swapped: -177.5645 76 76 iupac_m_486_> OE1/2 will be swapped: -178.4474 86 86 iupac_m_485_> OD1/2 will be swapped: -103.8746 103 103 iupac_m_487_> NH1/2 swapped: -178.9362 115 115 iupac_m_486_> OE1/2 will be swapped: -123.3398 121 121 iupac_m_486_> OE1/2 will be swapped: 110.9546 166 166 iupac_m_487_> NH1/2 swapped: 179.7238 178 178 iupac_m_487_> NH1/2 swapped: -178.8701 211 211 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 218 Number of all, selected real atoms : 1630 1630 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 20435 20435 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3622 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 975.0223 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 : 1663 0 0 0.005 0.005 12.223 1.000 2 Bond angle potential : 2254 0 2 1.950 1.950 169.34 1.000 3 Stereochemical cosine torsion poten: 1031 0 35 47.730 47.730 367.98 1.000 4 Stereochemical improper torsion pot: 657 0 0 1.162 1.162 21.602 1.000 5 Soft-sphere overlap restraints : 3622 0 0 0.001 0.001 0.77387 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 4670 0 0 0.080 0.080 38.154 1.000 10 Distance restraints 2 (N-O) : 4630 0 0 0.122 0.122 86.670 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: 217 0 0 3.429 3.429 30.097 1.000 14 Sidechain Chi_1 dihedral restraints: 172 0 0 52.703 52.703 3.6399 1.000 15 Sidechain Chi_2 dihedral restraints: 125 0 1 52.964 52.964 34.107 1.000 16 Sidechain Chi_3 dihedral restraints: 57 0 0 64.901 64.901 37.363 1.000 17 Sidechain Chi_4 dihedral restraints: 21 0 0 69.133 69.133 14.098 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) : 2945 0 0 0.312 0.312 58.663 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: 216 5 14 23.667 32.911 31.384 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1777 0 1 0.501 0.501 68.933 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf___224_> Open domain1.V99990010 # Heavy relative violation of each residue is written to: domain1.V99990010 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 16327.5439 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 5606 1G 2K C N 3 5 -71.76 -70.20 15.16 1.06 -62.90 163.96 21.79 1 2K 2K N CA 5 6 155.48 140.40 -40.80 2 5607 2K 3D C N 12 14 -61.55 -70.90 10.78 0.57 -63.30 175.08 21.51 2 3D 3D N CA 14 15 144.93 150.30 -40.00 3 5608 3D 4D C N 20 22 -83.33 -70.90 20.58 0.73 -63.30 154.60 20.34 3 4D 4D N CA 22 23 166.70 150.30 -40.00 4 5609 4D 5T C N 28 30 -103.09 -78.10 40.52 1.38 -63.20 141.93 20.86 4 5T 5T N CA 30 31 -178.31 149.80 -42.10 5 5711 106A 107D C N 765 767 75.48 -70.90 161.62 13.55 -70.90 161.62 13.55 5 107D 107D N CA 767 768 -141.17 150.30 150.30 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 5 24 75 99 146 170 186 253 276 288 << end of ENERGY. openf___224_> Open domain1.B99990010.pdb wrpdb___568_> Residues, atoms, selected atoms: 218 1630 1630 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- domain1.B99990001.pdb 1134.43152 domain1.B99990002.pdb 1059.23059 domain1.B99990003.pdb 930.89972 domain1.B99990004.pdb 905.69031 domain1.B99990005.pdb 999.68689 domain1.B99990006.pdb 1033.22363 domain1.B99990007.pdb 934.10492 domain1.B99990008.pdb 1022.23059 domain1.B99990009.pdb 927.88873 domain1.B99990010.pdb 975.02228 Dynamically allocated memory at finish [B,KiB,MiB]: 4229406 4130.279 4.033 Starting time : 2019/05/05 20:45:45 Closing time : 2019/05/05 20:50:25 Total CPU time [seconds] : 142.25