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 22:42:03 read_to_681_> topology.submodel read from topology file: 3 preppdf_455W> None of the non-bonded terms selected. 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 : 478 478 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 : 470.5479 Number of initially selected atoms : 468 Number of sufficiently violated selected atoms : 10 Neighbourhood, number of initial hot atoms : 4.00 89 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 2 :A MET --- 8 :A THR 7 2 14 :A LEU --- 15 :A THR 2 3 22 :A CYS --- 22 :A CYS 1 4 24 :A ARG --- 24 :A ARG 1 5 37 :A ARG --- 37 :A ARG 1 6 40 :A GLY --- 43 :A PRO 4 7 51 :A LYS --- 53 :A CYS 3 8 59 :A CYS --- 61 :A TYR 3 preppdf_455W> None of the non-bonded terms selected. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 468 171 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 478 183 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 Dynamic pairs routine : 5, NATM_SEL x NATM double loop Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : F F F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 170.8786 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 : 183 6 19 0.052 0.052 170.88 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 Detailed listing of all violated selected restraints: Csr, sel indices: 13 19 Bond length potential Atom indices : 21 20 IUPAC atoms : O C CHARMM atoms : O C Residue names: CYS CYS Residue numbs: 3 3 Mean : 1.2300 Stand dev : 0.0218 Force cns : 620.0001 Rel.violation: 5.1604 Feature, Ener: 1.3426 7.8572 1.0000 Csr, sel indices: 42 48 Bond length potential Atom indices : 49 48 IUPAC atoms : O C CHARMM atoms : O C Residue names: HIS HIS Residue numbs: 6 6 Mean : 1.2300 Stand dev : 0.0218 Force cns : 620.0001 Rel.violation: 4.8003 Feature, Ener: 1.3347 6.7988 1.0000 Csr, sel indices: 115 317 Bond length potential Atom indices : 313 312 IUPAC atoms : O C CHARMM atoms : O C Residue names: CYS CYS Residue numbs: 41 41 Mean : 1.2300 Stand dev : 0.0218 Force cns : 620.0001 Rel.violation: 5.0256 Feature, Ener: 1.3396 7.4519 1.0000 Csr, sel indices: 147 405 Bond length potential Atom indices : 398 397 IUPAC atoms : O C CHARMM atoms : O C Residue names: CYS CYS Residue numbs: 52 52 Mean : 1.2300 Stand dev : 0.0218 Force cns : 620.0001 Rel.violation: 4.7451 Feature, Ener: 1.3335 6.6434 1.0000 Csr, sel indices: 168 463 Bond length potential Atom indices : 455 454 IUPAC atoms : O C CHARMM atoms : O C Residue names: ASN ASN Residue numbs: 60 60 Mean : 1.2300 Stand dev : 0.0218 Force cns : 620.0001 Rel.violation: 4.8938 Feature, Ener: 1.3368 7.0663 1.0000 --------------------------------------------------------------------------------------- << end of ENERGY. Total CPU time [seconds] : 0.35