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): 2004/09/19 00:43:51.075 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: 13489 12353 >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 1 Number of all residues in MODEL : 162 Number of all, selected real atoms : 1267 1267 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 12353 12353 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 2444 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 : 941.2764 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 : 1295 0 0 0.004 0.004 7.0224 1.000 2 Bond angle potential : 1763 2 5 2.807 2.807 179.77 1.000 3 Stereochemical cosine torsion poten: 841 0 21 48.238 48.238 316.40 1.000 4 Stereochemical improper torsion pot: 524 0 0 1.193 1.193 15.469 1.000 5 Soft-sphere overlap restraints : 2444 0 0 0.001 0.001 0.57271 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) : 2700 0 0 0.262 0.262 80.067 1.000 10 Distance restraints 2 (N-O) : 2769 0 6 0.357 0.357 122.71 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: 161 0 0 4.061 4.061 31.145 1.000 14 Sidechain Chi_1 dihedral restraints: 132 0 2 72.396 72.396 28.652 1.000 15 Sidechain Chi_2 dihedral restraints: 97 0 1 68.864 68.864 43.132 1.000 16 Sidechain Chi_3 dihedral restraints: 47 0 0 70.131 70.131 33.589 1.000 17 Sidechain Chi_4 dihedral restraints: 15 0 0 78.076 78.076 10.672 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) : 1467 0 1 0.418 0.418 27.166 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: 160 12 10 26.795 51.017 27.050 1.000 26 Distance restraints 4 (SDCH-SDCH) : 382 0 0 0.563 0.563 17.863 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: hvdfr.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: 14590.8496 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 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4444 21L 22P C N 154 156 -69.51 -58.70 29.96 1.79 -64.50 149.83 11.45 1 22P 22P N CA 156 157 -2.55 -30.50 147.20 2 4492 69R 70S C N 536 538 -72.53 -72.40 20.30 1.19 -64.10 152.53 11.57 2 70S 70S N CA 538 539 172.70 152.40 -35.00 3 4512 89A 90A C N 681 683 151.79 -134.00 74.36 2.29 -62.50 -138.10 43.90 3 90A 90A N CA 683 684 151.74 147.00 -40.90 4 4514 91S 92L C N 692 694 -134.89 -63.50 92.19 12.29 -63.50 92.19 12.29 4 92L 92L N CA 694 695 17.12 -41.20 -41.20 5 4515 92L 93D C N 700 702 -68.81 -63.30 11.83 1.81 -96.50 166.99 7.03 5 93D 93D N CA 702 703 -50.47 -40.00 114.20 6 4524 101G 102G C N 765 767 110.77 78.70 61.34 0.95 -80.20 172.12 12.26 6 102G 102G N CA 767 768 141.61 -166.10 174.10 7 4544 121V 122P C N 923 925 -74.71 -58.70 44.97 2.70 -64.50 136.06 10.70 7 122P 122P N CA 925 926 11.52 -30.50 147.20 8 4563 140E 141L C N 1087 1089 -66.79 -63.50 8.53 1.05 -70.70 174.97 13.11 8 141L 141L N CA 1089 1090 -33.33 -41.20 141.60 9 4564 141L 142D C N 1095 1097 51.40 -63.30 135.04 16.94 -63.30 135.04 16.94 9 142D 142D N CA 1097 1098 -111.27 -40.00 -40.00 10 4581 158S 159A C N 1237 1239 -101.99 -134.00 37.92 0.91 -62.50 172.16 26.57 10 159A 159A N CA 1239 1240 126.68 147.00 -40.90 11 4582 159A 160S C N 1242 1244 -141.51 -136.60 23.05 1.06 -64.10 169.94 17.87 11 160S 160S N CA 1244 1245 173.72 151.20 -35.00 12 4583 160S 161S C N 1248 1250 -68.55 -72.40 6.94 0.53 -64.10 166.89 12.36 12 161S 161S N CA 1250 1251 158.17 152.40 -35.00 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 1 15 51 73 92 125 118 152 163 177 << end of ENERGY. Dynamically allocated memory at finish [B,kB,MB]: 10256197 10015.817 9.781 Starting time : 2004/09/19 00:43:51.075 Closing time : 2004/09/19 00:44:24.631 Total CPU time [seconds] : 33.45