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 22:41:55 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 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib 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 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 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open ../atom_files/pdb2abx.ent read_mo_297_> Segments, residues, atoms: 2 148 1102 read_mo_298_> Segment: 1 1 A 74 A 551 read_mo_298_> Segment: 2 1 B 74 B 551 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 74 550 564 0 0 223 patch_______> segment topology patched using RTF: 1 ; ILE ; NTER segments residues atoms bonds angles dihedrals impropers: 1 74 550 564 767 937 223 patch_______> segment topology patched using RTF: 74 ; GLY ; CTER segments residues atoms bonds angles dihedrals impropers: 1 74 551 565 769 938 224 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 74 551 565 769 938 224 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 148 1101 1129 769 938 447 patch_______> segment topology patched using RTF: 75 ; ILE ; NTER segments residues atoms bonds angles dihedrals impropers: 2 148 1101 1129 1536 1875 447 patch_______> segment topology patched using RTF: 148 ; GLY ; CTER segments residues atoms bonds angles dihedrals impropers: 2 148 1102 1130 1538 1876 448 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 148 1102 1130 1538 1876 448 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: 1102 0 preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). preppdf_455W> None of the non-bonded terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 0 0 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 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 : F F F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 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. << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1102 1102 1 6.0000 randomi_496_> Amplitude is > 0; randomization is done. define__645W> New number of symmetry segments, atom pairs: 1 297 preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). preppdf_455W> None of the non-bonded terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 0 0 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 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 : F F F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1785048.3750 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 : 0 0 0 0.000 0.000 0.0000 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 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 0.17850E+07 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. << end of ENERGY. openf___224_> Open define_symmetry-1.atm wrpdb___568_> Residues, atoms, selected atoms: 148 1102 1102 preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). preppdf_455W> None of the non-bonded terms selected. openf___224_> Open define_symmetry-2.atm wrpdb___568_> Residues, atoms, selected atoms: 148 1102 1102 preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). preppdf_455W> None of the non-bonded terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 0 0 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 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 : F F F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 0.0387 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 : 0 0 0 0.000 0.000 0.0000 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 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 0.38664E-01 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. << end of ENERGY. make_re_417_> Restraint type to be calculated: stereo r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 1130 1538 1848 432 Total number of restraints before, now : 0 4948 make_re_422_> Number of previous, current restraints : 0 4948 make_re_423_> Number of previous, current selected restraints: 0 4948 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1102 1102 1 3.0000 randomi_496_> Amplitude is > 0; randomization is done. Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4948 4948 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2294 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 300 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 16473106.0000 Current energy : 4171.4199 Optimizer exit status : 0 Number of iterations : 40 Number of calls to energy function : 91 Number of updates of dynamic contacts : 26 Number of non-updates of dynamic contacts : 66 Final maximal atomic shift : 0.001 Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4948 4948 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1505 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 3 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Maximal number of iterations (MAX_ITERATIONS) : 300 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 4171.4199 Current energy : 2968.6033 Number of iterations : 300 Number of calls to energy function : 301 Number of updates of dynamic contacts : 110 Number of non-updates of dynamic contacts : 191 Final maximal atomic shift : 0.137 TEMPERATURE : 293.000 EQUILIBRATE : 999999 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.200 Maximal energy, step : 4875.8989 1 Minimal energy, step : 2704.8838 145 Average energy, stand.dev. : 2992.3892 0.0000 Average atomic shift along one axis : 0.046 MODEL returned : FINAL Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4948 4948 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1538 Dynamic pairs routine : 2, NATM x NATM cell sorting Optimization method (OPTIMIZATON_METHOD) : 1 Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 Atomic shift for convergence (MIN_ATOM_SHIFT) : 0.010 Maximal number of iterations (MAX_ITERATIONS) : 300 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 All restraint types and their scaling factors : 1 Bond length potential : 1.0000 2 Bond angle potential : 1.0000 3 Stereochemical cosine torsion potential : 1.0000 4 Stereochemical improper torsion potentia : 1.0000 5 Soft-sphere overlap restraints : 1.0000 6 Lennard-Jones 6-12 potential : 1.0000 7 Coulomb point-point electrostatic potent : 1.0000 8 H-bonding potential : 1.0000 9 Distance restraints 1 (CA-CA) : 1.0000 10 Distance restraints 2 (N-O) : 1.0000 11 Mainchain Phi dihedral restraints : 1.0000 12 Mainchain Psi dihedral restraints : 1.0000 13 Mainchain Omega dihedral restraints : 1.0000 14 Sidechain Chi_1 dihedral restraints : 1.0000 15 Sidechain Chi_2 dihedral restraints : 1.0000 16 Sidechain Chi_3 dihedral restraints : 1.0000 17 Sidechain Chi_4 dihedral restraints : 1.0000 18 Disulfide distance restraints : 1.0000 19 Disulfide angle restraints : 1.0000 20 Disulfide dihedral angle restraints : 1.0000 21 Lower bound distance restraints : 1.0000 22 Upper bound distance restraints : 1.0000 23 Distance restraints 3 (SDCH-MNCH) : 1.0000 24 Sidechain Chi_5 dihedral restraints : 1.0000 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 36 GBSA implicit solvent potential : 1.0000 37 EM density fitting potential : 1.0000 38 SAXS restraints : 1.0000 39 Symmetry restraints : 1.0000 Initial value of energy before optimization : 2968.6033 Current energy : 699.5568 Optimizer exit status : 0 Number of iterations : 57 Number of calls to energy function : 116 Number of updates of dynamic contacts : 8 Number of non-updates of dynamic contacts : 109 Final maximal atomic shift : 0.008 openf___224_> Open define_symmetry-3.atm wrpdb___568_> Residues, atoms, selected atoms: 148 1102 1102 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 148 Number of all, selected real atoms : 1102 1102 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 4948 4948 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1536 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 : 699.5576 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 : 1130 0 0 0.004 0.004 5.2017 1.000 2 Bond angle potential : 1538 0 0 2.042 2.042 110.22 1.000 3 Stereochemical cosine torsion poten: 1848 0 59 52.716 52.716 567.83 1.000 4 Stereochemical improper torsion pot: 432 0 0 1.107 1.107 10.530 1.000 5 Soft-sphere overlap restraints : 1536 0 0 0.004 0.004 3.3567 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 : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 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 2.4241 1.000 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. report______> Distribution of short non-bonded contacts: 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 16 61 59 67 83 84 98 119 100 << end of ENERGY. report__> Symmetry breaking contribution to -Ln[Molec.pdf]: All Diff larger than cutoff are reported: 0.30000 Atm1A Atm2A Atm1B Atm2B WghA WghB DistA DistB Diff Term ------------------------------------------------------------------------ openf___224_> Open define_symmetry-3.atm read_mo_297_> Segments, residues, atoms: 1 74 551 read_mo_298_> Segment: 1 1 A 74 A 551 openf___224_> Open define_symmetry-3.atm read_mo_297_> Segments, residues, atoms: 1 74 551 read_mo_298_> Segment: 1 1 B 74 B 551 SUPERPOSITION OF TWO 3D STRUCTURES (MODEL2 onto MODEL): Least-squares superposition: PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2 Superposition done : T Refine using local substructures : T Numb of residues in MODEL : 74 Numb of atoms/sel atoms in MODEL : 551 297 Numb of residues in MODEL2 : 74 Numb of atoms in MODEL2 : 551 Equivalences refinement : F Numb of aligned equiv positions : 297 Numb of aligned equiv distances : 43956 RMS before superposition : 31.1231 RMS after superposition : 0.0120 DRMS : 0.0074 Distance cutoff : 3.5000 Numb of equiv cutoff positions : 297 Numb of equiv cutoff distances : 43956 Cutoff RMS after superposition : 0.0120 Cutoff DRMS : 0.0074 X_new = Rotation * X + Translation Rotation matrix : -0.9995 -0.0001 -0.0312 0.0036 -0.9939 -0.1103 -0.0310 -0.1104 0.9934 Translation vector: 73.0683 107.5786 8.2662 Starting time : 2016/04/05 22:41:55 Closing time : 2016/04/05 22:41:57 Total CPU time [seconds] : 2.48