MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:42:02 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 $(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]: 393422 384.201 0.375 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 395022 385.764 0.377 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 399002 389.650 0.381 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 401002 391.604 0.382 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 404002 394.533 0.385 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 408502 398.928 0.390 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 414074 404.369 0.395 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 416874 407.104 0.398 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 421074 411.205 0.402 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 427374 417.357 0.408 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 430146 420.064 0.410 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 431546 421.432 0.412 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open toxin.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 435147 424.948 0.415 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 436568 426.336 0.416 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 438018 427.752 0.418 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 471002 459.963 0.449 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 471282 460.236 0.449 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 471574 460.521 0.450 Read the alignment from file : toxin.ali Total number of alignment positions: 74 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2abx 74 1 2abx alpha-bungarotoxin openf___224_> Open ../atom_files/pdb2ctx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 494599 483.007 0.472 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 494599 483.007 0.472 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 494770 483.174 0.472 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495620 484.004 0.473 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 496878 485.232 0.474 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 498782 487.092 0.476 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 498782 487.092 0.476 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 498872 487.180 0.476 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 501728 489.969 0.478 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 501728 489.969 0.478 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 501863 490.101 0.479 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506147 494.284 0.483 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 506147 494.284 0.483 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 506345 494.478 0.483 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 512771 500.753 0.489 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 512771 500.753 0.489 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 513068 501.043 0.489 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 512807 500.788 0.489 openf___224_> Open ../atom_files/pdb2abx.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 536732 524.152 0.512 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 536732 524.152 0.512 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 536903 524.319 0.512 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 537753 525.149 0.513 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 539011 526.378 0.514 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 540915 528.237 0.516 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 540915 528.237 0.516 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 541005 528.325 0.516 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543861 531.114 0.519 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543861 531.114 0.519 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 543996 531.246 0.519 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 548280 535.430 0.523 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 548280 535.430 0.523 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 548478 535.623 0.523 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 554904 541.898 0.529 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 554904 541.898 0.529 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 555201 542.188 0.529 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 554967 541.960 0.529 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 580657 567.048 0.554 malign3_328_> Initial framework positions: 71 malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 1 2 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 3.5000 Gap introduction penalty : 0.0000 Gap extension penalty : 1.7500 Numb of residues in framework : 71 openf___224_> Open toxin.ali Read the alignment from file : toxin.ali Total number of alignment positions: 76 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ctx 71 1 2ctx alpha-cobratoxin 2 2abx 74 1 2abx alpha-bungarotoxin 3 1fas 61 1 1fas fasciculin 1 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 599364 585.316 0.572 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 646992 631.828 0.617 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 653896 638.570 0.624 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 467 477 0 0 193 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 673872 658.078 0.643 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 61 467 477 643 768 193 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 695408 679.109 0.663 patch_______> segment topology patched using RTF: 61 ; TYR ; CTER segments residues atoms bonds angles dihedrals impropers: 1 61 468 478 645 770 194 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 61 468 478 645 770 194 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 2 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 377 91 openf___224_> Open 1fas.noSS wrpdb___568_> Residues, atoms, selected atoms: 61 468 468 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 700180 683.770 0.668 patch_______> segment topology patched using RTF: 3 22 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 468 479 647 773 194 patch_______> segment topology patched using RTF: 17 39 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 468 480 649 776 194 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 700428 684.012 0.668 patch_______> segment topology patched using RTF: 41 52 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 468 481 651 779 194 patch_______> segment topology patched using RTF: 53 59 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 61 468 482 653 782 194 patch_s_522_> Number of disulfides patched in MODEL: 4 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 807457 788.532 0.770 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 815649 796.532 0.778 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 832033 812.532 0.793 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 864801 844.532 0.825 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 897569 876.532 0.856 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 482 653 769 189 Total number of restraints before, now : 0 2093 make_re_422_> Number of previous, current restraints : 0 2093 make_re_423_> Number of previous, current selected restraints: 0 2093 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 1031756 1007.574 0.984 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1335592 1304.289 1.274 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 468 468 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 2093 2093 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 394 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 : 1817385.5000 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 : 478 0 0 0.021 0.021 58.615 1.000 2 Bond angle potential : 645 0 0 2.915 2.915 95.890 1.000 3 Stereochemical cosine torsion poten: 757 5 55 64.233 64.233 261.31 1.000 4 Stereochemical improper torsion pot: 189 3 3 8.808 8.808 249.59 1.000 5 Soft-sphere overlap restraints : 394 27 34 0.164 0.164 1249.3 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 4 4 4 51.214 51.214 0.18150E+07 1.000 19 Disulfide angle restraints : 8 6 6 47.798 47.798 403.65 1.000 20 Disulfide dihedral angle restraints: 12 2 3 52.662 52.662 24.727 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 3 : Stereochemical cosine torsion 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 1507 30P 30P CA CB 234 236 -34.55 34.59 -69.14 6.44 34.59 -69.14 6.44 2 1526 31P 31P CA CB 241 243 -34.53 34.59 -69.12 6.44 34.59 -69.12 6.44 3 1649 42P 42P CA CB 315 317 -34.55 34.59 -69.14 6.44 34.59 -69.14 6.44 4 1668 43P 43P CA CB 322 324 -34.53 34.59 -69.12 6.44 34.59 -69.12 6.44 5 1826 56P 56P CA CB 419 421 -34.54 34.59 -69.13 6.44 34.59 -69.13 6.44 ------------------------------------------------------------------------------------------------- Feature 18 : Disulfide distance restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 479 3C 22C SG SG 19 160 69.05 2.03 67.03 1623.00 2.03 67.03 1623.00 2 480 17C 39C SG SG 127 301 68.38 2.03 66.35 1606.62 2.03 66.35 1606.62 3 481 41C 52C SG SG 311 396 37.48 2.03 35.45 858.43 2.03 35.45 858.43 4 482 53C 59C SG SG 402 445 20.47 2.03 18.44 446.55 2.03 18.44 446.55 ------------------------------------------------------------------------------------------------- Feature 19 : Disulfide angle restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 508 3C 3C CB SG 18 19 134.66 103.30 31.36 8.58 103.30 31.36 8.58 2 660 17C 17C CB SG 126 127 131.99 103.30 28.69 7.85 103.30 28.69 7.85 ------------------------------------------------------------------------------------------------- Feature 20 : Disulfide dihedral angle restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1894 3C 3C CB SG 18 19 175.47 180.00 -4.53 8.15 180.00 -4.53 8.15 2 1897 17C 17C CB SG 126 127 155.73 180.00 -24.27 6.82 180.00 -24.27 6.82 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 121 124 2.247 serious non-bonded atom clash: 148 151 2.247 serious non-bonded atom clash: 226 235 1.988 serious non-bonded atom clash: 228 235 2.150 serious non-bonded atom clash: 228 237 1.960 serious non-bonded atom clash: 229 235 1.726 serious non-bonded atom clash: 229 237 2.245 serious non-bonded atom clash: 263 268 2.249 serious non-bonded atom clash: 311 316 2.013 serious non-bonded atom clash: 376 381 2.249 serious non-bonded atom clash: 415 420 1.948 serious non-bonded atom clash: 453 456 2.247 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: 5 1 6 6 2 9 4 17 29 58 18 11 16 28 19 << end of ENERGY. openf___224_> Open 1fas.noSS Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1335592 1304.289 1.274 read_mo_297_> Segments, residues, atoms: 1 61 468 read_mo_298_> Segment: 1 1 61 468 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1401689 1368.837 1.337 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1434457 1400.837 1.368 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1467225 1432.837 1.399 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1532761 1496.837 1.462 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 482 653 769 189 Total number of restraints before, now : 2093 4186 make_re_422_> Number of previous, current restraints : 2093 4186 make_re_423_> Number of previous, current selected restraints: 2093 4186 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 468 468 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4186 4186 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 395 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 : 3633510.5000 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 : 956 0 0 0.021 0.021 117.47 1.000 2 Bond angle potential : 1290 0 0 2.915 2.915 191.76 1.000 3 Stereochemical cosine torsion poten: 1514 10 110 64.231 64.231 522.62 1.000 4 Stereochemical improper torsion pot: 378 6 6 8.810 8.810 499.37 1.000 5 Soft-sphere overlap restraints : 395 27 34 0.164 0.164 1249.3 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 18 Disulfide distance restraints : 8 8 8 51.214 51.214 0.36301E+07 1.000 19 Disulfide angle restraints : 16 12 12 47.799 47.799 807.33 1.000 20 Disulfide dihedral angle restraints: 24 4 6 52.670 52.670 49.451 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 3 : Stereochemical cosine torsion 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 1507 30P 30P CA CB 234 236 -34.52 34.59 -69.11 6.43 34.59 -69.11 6.43 2 1526 31P 31P CA CB 241 243 -34.48 34.59 -69.07 6.43 34.59 -69.07 6.43 3 1649 42P 42P CA CB 315 317 -34.57 34.59 -69.16 6.44 34.59 -69.16 6.44 4 1668 43P 43P CA CB 322 324 -34.52 34.59 -69.11 6.43 34.59 -69.11 6.43 5 1826 56P 56P CA CB 419 421 -34.62 34.59 -69.21 6.45 34.59 -69.21 6.45 6 3600 30P 30P CA CB 234 236 -34.52 34.59 -69.11 6.43 34.59 -69.11 6.43 7 3619 31P 31P CA CB 241 243 -34.48 34.59 -69.07 6.43 34.59 -69.07 6.43 8 3742 42P 42P CA CB 315 317 -34.57 34.59 -69.16 6.44 34.59 -69.16 6.44 9 3761 43P 43P CA CB 322 324 -34.52 34.59 -69.11 6.43 34.59 -69.11 6.43 10 3919 56P 56P CA CB 419 421 -34.62 34.59 -69.21 6.45 34.59 -69.21 6.45 ------------------------------------------------------------------------------------------------- Feature 18 : Disulfide distance restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 479 3C 22C SG SG 19 160 69.05 2.03 67.03 1623.00 2.03 67.03 1623.00 2 480 17C 39C SG SG 127 301 68.38 2.03 66.35 1606.62 2.03 66.35 1606.62 3 481 41C 52C SG SG 311 396 37.48 2.03 35.45 858.42 2.03 35.45 858.42 4 482 53C 59C SG SG 402 445 20.47 2.03 18.44 446.54 2.03 18.44 446.54 5 2572 3C 22C SG SG 19 160 69.05 2.03 67.03 1623.00 2.03 67.03 1623.00 6 2573 17C 39C SG SG 127 301 68.38 2.03 66.35 1606.62 2.03 66.35 1606.62 7 2574 41C 52C SG SG 311 396 37.48 2.03 35.45 858.42 2.03 35.45 858.42 8 2575 53C 59C SG SG 402 445 20.47 2.03 18.44 446.54 2.03 18.44 446.54 ------------------------------------------------------------------------------------------------- Feature 19 : Disulfide angle restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 508 3C 3C CB SG 18 19 134.68 103.30 31.38 8.58 103.30 31.38 8.58 2 660 17C 17C CB SG 126 127 131.99 103.30 28.69 7.85 103.30 28.69 7.85 3 2601 3C 3C CB SG 18 19 134.68 103.30 31.38 8.58 103.30 31.38 8.58 4 2753 17C 17C CB SG 126 127 131.99 103.30 28.69 7.85 103.30 28.69 7.85 ------------------------------------------------------------------------------------------------- Feature 20 : Disulfide dihedral angle restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1894 3C 3C CB SG 18 19 175.47 180.00 -4.53 8.15 180.00 -4.53 8.15 2 1897 17C 17C CB SG 126 127 155.73 180.00 -24.27 6.81 180.00 -24.27 6.81 3 3987 3C 3C CB SG 18 19 175.47 180.00 -4.53 8.15 180.00 -4.53 8.15 4 3990 17C 17C CB SG 126 127 155.73 180.00 -24.27 6.81 180.00 -24.27 6.81 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 121 124 2.247 serious non-bonded atom clash: 148 151 2.247 serious non-bonded atom clash: 226 235 1.988 serious non-bonded atom clash: 228 235 2.150 serious non-bonded atom clash: 228 237 1.961 serious non-bonded atom clash: 229 235 1.726 serious non-bonded atom clash: 229 237 2.245 serious non-bonded atom clash: 263 268 2.249 serious non-bonded atom clash: 311 316 2.013 serious non-bonded atom clash: 376 381 2.248 serious non-bonded atom clash: 415 420 1.947 serious non-bonded atom clash: 453 456 2.247 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: 5 1 6 6 2 9 4 17 29 58 18 11 16 28 19 << end of ENERGY. Dynamically allocated memory at finish [B,KiB,MiB]: 1532200 1496.289 1.461 Starting time : 2016/04/05 22:42:02 Closing time : 2016/04/05 22:42:02 Total CPU time [seconds] : 0.39