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 22:42:05 read_to_681_> topology.submodel read from topology file: 7 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 20 61 atom names : CA +CA atom indices : 61 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 1 atom names : -CA CA +CA atom indices : 0 1 2 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 20 61 atom names : -CA CA +CA atom indices : 60 61 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 17 1 atom names : -CA CA atom indices : 0 1 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 61 Number of all, selected real atoms : 61 61 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 177 177 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 : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 714.6531 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 : 60 2 2 0.161 0.161 108.50 1.000 2 Bond angle potential : 59 41 58 57.370 57.370 591.52 1.000 3 Stereochemical cosine torsion poten: 58 0 0 118.285 118.285 14.634 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. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 61 1T 2M CA CA 1 2 105.85 61.00 44.85 4.56 61.00 44.85 4.56 2 62 2M 3C CA CA 2 3 137.84 61.00 76.84 7.81 61.00 76.84 7.81 3 63 3C 4Y CA CA 3 4 108.79 61.00 47.79 4.86 61.00 47.79 4.86 4 64 4Y 5S CA CA 4 5 106.32 61.00 45.32 4.60 61.00 45.32 4.60 5 65 5S 6H CA CA 5 6 139.02 61.00 78.02 7.93 61.00 78.02 7.93 6 67 7T 8T CA CA 7 8 123.15 61.00 62.15 6.31 61.00 62.15 6.31 7 70 10S 11R CA CA 10 11 118.85 61.00 57.85 5.88 61.00 57.85 5.88 8 72 12A 13I CA CA 12 13 131.12 61.00 70.12 7.12 61.00 70.12 7.12 9 73 13I 14L CA CA 13 14 136.12 61.00 75.12 7.63 61.00 75.12 7.63 10 74 14L 15T CA CA 14 15 119.86 61.00 58.86 5.98 61.00 58.86 5.98 11 77 17C 18G CA CA 17 18 109.80 61.00 48.80 4.96 61.00 48.80 4.96 12 79 19E 20N CA CA 19 20 128.20 61.00 67.20 6.83 61.00 67.20 6.83 13 80 20N 21S CA CA 20 21 127.78 61.00 66.78 6.79 61.00 66.78 6.79 14 81 21S 22C CA CA 21 22 118.43 61.00 57.43 5.84 61.00 57.43 5.84 15 82 22C 23Y CA CA 22 23 133.85 61.00 72.85 7.40 61.00 72.85 7.40 16 83 23Y 24R CA CA 23 24 116.56 61.00 55.56 5.65 61.00 55.56 5.65 17 84 24R 25K CA CA 24 25 123.63 61.00 62.63 6.36 61.00 62.63 6.36 18 85 25K 26S CA CA 25 26 142.53 61.00 81.53 8.28 61.00 81.53 8.28 19 86 26S 27R CA CA 26 27 106.68 61.00 45.68 4.64 61.00 45.68 4.64 20 88 28R 29H CA CA 28 29 125.30 61.00 64.30 6.53 61.00 64.30 6.53 21 89 29H 30P CA CA 29 30 128.66 61.00 67.66 6.87 61.00 67.66 6.87 22 92 32K 33M CA CA 32 33 118.83 61.00 57.83 5.88 61.00 57.83 5.88 23 93 33M 34V CA CA 33 34 109.50 61.00 48.50 4.93 61.00 48.50 4.93 24 95 35L 36G CA CA 35 36 147.05 61.00 86.05 8.74 61.00 86.05 8.74 25 96 36G 37R CA CA 36 37 128.20 61.00 67.20 6.83 61.00 67.20 6.83 26 97 37R 38G CA CA 37 38 146.66 61.00 85.66 8.70 61.00 85.66 8.70 27 98 38G 39C CA CA 38 39 122.27 61.00 61.27 6.23 61.00 61.27 6.23 28 99 39C 40G CA CA 39 40 132.10 61.00 71.10 7.22 61.00 71.10 7.22 29 100 40G 41C CA CA 40 41 113.56 61.00 52.56 5.34 61.00 52.56 5.34 30 101 41C 42P CA CA 41 42 120.01 61.00 59.01 6.00 61.00 59.01 6.00 31 102 42P 43P CA CA 42 43 121.53 61.00 60.53 6.15 61.00 60.53 6.15 32 103 43P 44G CA CA 43 44 125.44 61.00 64.44 6.55 61.00 64.44 6.55 33 104 44G 45D CA CA 44 45 135.53 61.00 74.53 7.57 61.00 74.53 7.57 34 107 47Y 48L CA CA 47 48 128.35 61.00 67.35 6.84 61.00 67.35 6.84 35 108 48L 49E CA CA 48 49 115.09 61.00 54.09 5.50 61.00 54.09 5.50 36 109 49E 50V CA CA 49 50 120.10 61.00 59.10 6.00 61.00 59.10 6.00 37 110 50V 51K CA CA 50 51 116.33 61.00 55.33 5.62 61.00 55.33 5.62 38 111 51K 52C CA CA 51 52 126.10 61.00 65.10 6.61 61.00 65.10 6.61 39 112 52C 53C CA CA 52 53 134.48 61.00 73.48 7.47 61.00 73.48 7.47 40 114 54T 55S CA CA 54 55 155.45 61.00 94.45 9.60 61.00 94.45 9.60 41 116 56P 57D CA CA 56 57 113.36 61.00 52.36 5.32 61.00 52.36 5.32 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 0 0 0 0 0 0 0 0 0 0 << end of ENERGY. read_to_681_> topology.submodel read from topology file: 3 >> ENERGY; Differences between the model's features and restraints: 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 : 177 177 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 804 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 : 1373.8374 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 : 60 2 2 0.161 0.161 108.50 1.000 2 Bond angle potential : 59 41 58 57.370 57.370 591.52 1.000 3 Stereochemical cosine torsion poten: 58 0 0 118.285 118.285 14.634 1.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 1.000 5 Soft-sphere overlap restraints : 804 4 4 0.083 0.083 659.18 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. ------------------------------------------------------------------------------------------------- Feature 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 61 1T 2M CA CA 2 9 105.85 61.00 44.85 4.56 61.00 44.85 4.56 2 62 2M 3C CA CA 9 17 137.84 61.00 76.84 7.81 61.00 76.84 7.81 3 63 3C 4Y CA CA 17 23 108.79 61.00 47.79 4.86 61.00 47.79 4.86 4 64 4Y 5S CA CA 23 35 106.32 61.00 45.32 4.60 61.00 45.32 4.60 5 65 5S 6H CA CA 35 41 139.02 61.00 78.02 7.93 61.00 78.02 7.93 6 67 7T 8T CA CA 51 58 123.15 61.00 62.15 6.31 61.00 62.15 6.31 7 70 10S 11R CA CA 72 78 118.85 61.00 57.85 5.88 61.00 57.85 5.88 8 72 12A 13I CA CA 89 94 131.12 61.00 70.12 7.12 61.00 70.12 7.12 9 73 13I 14L CA CA 94 102 136.12 61.00 75.12 7.63 61.00 75.12 7.63 10 74 14L 15T CA CA 102 110 119.86 61.00 58.86 5.98 61.00 58.86 5.98 11 77 17C 18G CA CA 125 131 109.80 61.00 48.80 4.96 61.00 48.80 4.96 12 79 19E 20N CA CA 135 144 128.20 61.00 67.20 6.83 61.00 67.20 6.83 13 80 20N 21S CA CA 144 152 127.78 61.00 66.78 6.79 61.00 66.78 6.79 14 81 21S 22C CA CA 152 158 118.43 61.00 57.43 5.84 61.00 57.43 5.84 15 82 22C 23Y CA CA 158 164 133.85 61.00 72.85 7.40 61.00 72.85 7.40 16 83 23Y 24R CA CA 164 176 116.56 61.00 55.56 5.65 61.00 55.56 5.65 17 84 24R 25K CA CA 176 187 123.63 61.00 62.63 6.36 61.00 62.63 6.36 18 85 25K 26S CA CA 187 196 142.53 61.00 81.53 8.28 61.00 81.53 8.28 19 86 26S 27R CA CA 196 202 106.68 61.00 45.68 4.64 61.00 45.68 4.64 20 88 28R 29H CA CA 213 224 125.30 61.00 64.30 6.53 61.00 64.30 6.53 21 89 29H 30P CA CA 224 234 128.66 61.00 67.66 6.87 61.00 67.66 6.87 22 92 32K 33M CA CA 248 257 118.83 61.00 57.83 5.88 61.00 57.83 5.88 23 93 33M 34V CA CA 257 265 109.50 61.00 48.50 4.93 61.00 48.50 4.93 24 95 35L 36G CA CA 272 280 147.05 61.00 86.05 8.74 61.00 86.05 8.74 25 96 36G 37R CA CA 280 284 128.20 61.00 67.20 6.83 61.00 67.20 6.83 26 97 37R 38G CA CA 284 295 146.66 61.00 85.66 8.70 61.00 85.66 8.70 27 98 38G 39C CA CA 295 299 122.27 61.00 61.27 6.23 61.00 61.27 6.23 28 99 39C 40G CA CA 299 305 132.10 61.00 71.10 7.22 61.00 71.10 7.22 29 100 40G 41C CA CA 305 309 113.56 61.00 52.56 5.34 61.00 52.56 5.34 30 101 41C 42P CA CA 309 315 120.01 61.00 59.01 6.00 61.00 59.01 6.00 31 102 42P 43P CA CA 315 322 121.53 61.00 60.53 6.15 61.00 60.53 6.15 32 103 43P 44G CA CA 322 329 125.44 61.00 64.44 6.55 61.00 64.44 6.55 33 104 44G 45D CA CA 329 333 135.53 61.00 74.53 7.57 61.00 74.53 7.57 34 107 47Y 48L CA CA 349 361 128.35 61.00 67.35 6.84 61.00 67.35 6.84 35 108 48L 49E CA CA 361 369 115.09 61.00 54.09 5.50 61.00 54.09 5.50 36 109 49E 50V CA CA 369 378 120.10 61.00 59.10 6.00 61.00 59.10 6.00 37 110 50V 51K CA CA 378 385 116.33 61.00 55.33 5.62 61.00 55.33 5.62 38 111 51K 52C CA CA 385 394 126.10 61.00 65.10 6.61 61.00 65.10 6.61 39 112 52C 53C CA CA 394 400 134.48 61.00 73.48 7.47 61.00 73.48 7.47 40 114 54T 55S CA CA 406 413 155.45 61.00 94.45 9.60 61.00 94.45 9.60 41 116 56P 57D CA CA 419 426 113.36 61.00 52.36 5.32 61.00 52.36 5.32 report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 19 160 2.032 serious non-bonded atom clash: 127 301 2.020 serious non-bonded atom clash: 311 396 2.009 serious non-bonded atom clash: 402 445 2.024 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: 4 0 0 0 0 0 1 5 17 23 29 31 45 49 64 << end of ENERGY. Total CPU time [seconds] : 0.36