MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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 synth.compbio.ucsf.edu 2.6.6-1.435.2.3smp i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/07/16 11:58:13.065 TOP_________> 2 2 READ_MODEL FILE = 'pseudo.atm' openf5__224_> Open 11 OLD SEQUENTIAL pseudo.atm openf5__224_> Open 11 OLD SEQUENTIAL pseudo.atm rdatm___297_> Segments, residues, atoms: 1 1 5 rdatm___298_> Segment: 1 1 1 5 TOP_________> 3 3 READ_RESTRAINTS FILE = 'pseudo.rsr' openf5__224_> Open 11 OLD SEQUENTIAL pseudo.rsr openf5__224_> Open 11 OLD SEQUENTIAL pseudo.rsr rdcsr2__307_> Number of restraints read : 1 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 openf5__224_> Open 11 OLD SEQUENTIAL pseudo.rsr openf5__224_> Open 11 OLD SEQUENTIAL pseudo.rsr rdcsr2__307_> Number of restraints read : 1 Number of excluded pairs read: 0 Number of pseudo atoms read : 1 rdcsrs__304_> Restraints in memory, selected restraints: 1 1 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 1 TOP_________> 4 4 SET DYNAMIC_SPHERE = OFF TOP_________> 5 5 ENERGY >> ENERGY; Differences between the model's features and restraints: preppdf_455W> None of the non-bonded terms selected. ID1, ID2 : 1 1 Number of all residues in MODEL : 1 Number of all, selected real atoms : 5 5 Number of all, selected pseudo atoms : 1 1 Number of all static, selected restraints : 1 1 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 Dynamic pairs routine : 1, NATM 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 SCHEDULE_STEP, N_SCHEDULE : 1 1 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 8851.4873 Symmetry term within 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 0.00000 1.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.00000 1.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.00000 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.00000 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.00000 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.00000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.00000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.00000 1.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.00000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.00000 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 13 Mainchain Omega dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.00000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.00000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.00000 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 25 Phi/Psi pair of dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.00000 1.000 27 Distance restraints 5 (X-Y) : 1 1 1 17.321 17.321 8851.5 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.00000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.00000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.00000 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 27 : Distance restraints 5 (X-Y) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1 1A 1A N PSD 5 6 17.32 0.00 17.32 173.21 0.00 17.32 173.21 << end of ENERGY. TOP_________> 6 6 OPTIMIZE preppdf_455W> None of the non-bonded terms selected. ID1, ID2 : 1 1 Number of all residues in MODEL : 1 Number of all, selected real atoms : 5 5 Number of all, selected pseudo atoms : 1 1 Number of all static, selected restraints : 1 1 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 0 Dynamic pairs routine : 1, NATM x NATM double loop 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) : 200 RESIDUE_SPAN_RANGE : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : F F F F F SCHEDULE_STEP, N_SCHEDULE : 1 1 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 Initial value of energy before optimization : 8851.4873 Current energy : 0.0000 Symmetry term within energy : 0.0000 Optimizer exit status : 0 Number of iterations : 2 Number of calls to energy function : 6 Number of updates of dynamic contacts : 0 Number of non-updates of dynamic contacts : 7 Final maximal atomic shift : 0.001 TOP_________> 7 7 WRITE_MODEL FILE = 'pseudoout.atm' openf5__224_> Open 14 UNKNOWN SEQUENTIAL pseudoout.atm wrpdb2__568_> Residues, atoms, selected atoms: 1 5 5 Dynamically allocated memory at finish [B,kB,MB]: 3527129 3444.462 3.364 Starting time : 2004/07/16 11:58:13.065 Closing time : 2004/07/16 11:58:13.618 Total CPU time [seconds] : 0.52