MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, 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 synth.compbio.ucsf.edu 2.6.8-1.521smp i686 Date and time of compilation : 09/12/2004 21:24:59 Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 18:13:48.013 check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 11766 10866 >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 1 Number of all residues in MODEL : 131 Number of all, selected real atoms : 1034 1034 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 10866 10866 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1985 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 : 0 200 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 10 10 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 596.8284 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 : 1048 0 0 0.004 0.004 5.8882 1.000 2 Bond angle potential : 1412 0 0 1.423 1.423 56.021 1.000 3 Stereochemical cosine torsion poten: 631 0 21 52.716 52.716 296.93 1.000 4 Stereochemical improper torsion pot: 421 0 0 0.945 0.945 7.8781 1.000 5 Soft-sphere overlap restraints : 1985 0 0 0.001 0.001 0.31113 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) : 2077 0 0 0.084 0.084 16.472 1.000 10 Distance restraints 2 (N-O) : 2220 0 0 0.117 0.117 30.590 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: 130 0 0 3.553 3.553 19.355 1.000 14 Sidechain Chi_1 dihedral restraints: 115 0 1 60.273 60.273 11.314 1.000 15 Sidechain Chi_2 dihedral restraints: 79 0 1 61.448 61.448 30.453 1.000 16 Sidechain Chi_3 dihedral restraints: 37 0 0 61.581 61.581 26.527 1.000 17 Sidechain Chi_4 dihedral restraints: 18 0 0 92.126 92.126 12.428 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) : 1715 0 0 0.302 0.302 30.028 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: 129 0 5 20.850 22.492 -0.12920E-01 1.000 26 Distance restraints 4 (SDCH-SDCH) : 834 0 2 0.626 0.626 52.647 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 # Heavy relative violation of each residue is written to: blbp.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: 9250.2637 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 8 14 31 64 58 86 92 106 132 124 << end of ENERGY. Dynamically allocated memory at finish [B,kB,MB]: 8553515 8353.042 8.157 Starting time : 2004/09/17 18:13:48.013 Closing time : 2004/09/17 18:14:36.171 Total CPU time [seconds] : 47.67