Starting phenix.real_space_refine on Thu Jul 2 21:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsp_18638/07_2026/8qsp_18638.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 128 5.16 5 C 6358 2.51 5 N 1727 2.21 5 O 1957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2520 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2560 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 21, 'TRANS': 313} Chain: "C" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2520 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "D" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2570 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 21, 'TRANS': 314} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.40, per 1000 atoms: 0.24 Number of scatterers: 10174 At special positions: 0 Unit cell: (87.15, 90.47, 162.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 128 16.00 O 1957 8.00 N 1727 7.00 C 6358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=58, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS B1174 " distance=2.02 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C1071 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C1033 " distance=2.03 Simple disulfide: pdb=" SG CYS C 953 " - pdb=" SG CYS C 960 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1095 " - pdb=" SG CYS C1119 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1146 " distance=2.03 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1134 " distance=2.03 Simple disulfide: pdb=" SG CYS C1136 " - pdb=" SG CYS C1161 " distance=2.03 Simple disulfide: pdb=" SG CYS C1152 " - pdb=" SG CYS C1181 " distance=2.03 Simple disulfide: pdb=" SG CYS C1165 " - pdb=" SG CYS C1206 " distance=2.03 Simple disulfide: pdb=" SG CYS C1174 " - pdb=" SG CYS D1174 " distance=2.03 Simple disulfide: pdb=" SG CYS C1185 " - pdb=" SG CYS C1196 " distance=2.03 Simple disulfide: pdb=" SG CYS C1189 " - pdb=" SG CYS C1228 " distance=2.03 Simple disulfide: pdb=" SG CYS C1210 " - pdb=" SG CYS C1224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 903 " - pdb=" SG CYS D1036 " distance=2.03 Simple disulfide: pdb=" SG CYS D 925 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 934 " - pdb=" SG CYS D1033 " distance=2.03 Simple disulfide: pdb=" SG CYS D 953 " - pdb=" SG CYS D 960 " distance=2.03 Simple disulfide: pdb=" SG CYS D1081 " - pdb=" SG CYS D1124 " distance=2.03 Simple disulfide: pdb=" SG CYS D1095 " - pdb=" SG CYS D1119 " distance=2.03 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1146 " distance=2.03 Simple disulfide: pdb=" SG CYS D1126 " - pdb=" SG CYS D1134 " distance=2.04 Simple disulfide: pdb=" SG CYS D1136 " - pdb=" SG CYS D1161 " distance=2.03 Simple disulfide: pdb=" SG CYS D1152 " - pdb=" SG CYS D1181 " distance=2.03 Simple disulfide: pdb=" SG CYS D1165 " - pdb=" SG CYS D1206 " distance=2.03 Simple disulfide: pdb=" SG CYS D1185 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1189 " - pdb=" SG CYS D1228 " distance=2.03 Simple disulfide: pdb=" SG CYS D1210 " - pdb=" SG CYS D1224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 441.0 milliseconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 25.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.658A pdb=" N PHE A1047 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.708A pdb=" N TRP A1065 " --> pdb=" O PHE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1085 through 1096 removed outlier: 4.413A pdb=" N SER A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP A1090 " --> pdb=" O PHE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1102 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.984A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1125 Processing helix chain 'A' and resid 1130 through 1149 removed outlier: 3.865A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 3.979A pdb=" N TYR A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1043 through 1048 removed outlier: 3.825A pdb=" N PHE B1047 " --> pdb=" O VAL B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1065 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1100 removed outlier: 4.843A pdb=" N ILE B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B1098 " --> pdb=" O GLN B1094 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS B1099 " --> pdb=" O CYS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1110 removed outlier: 3.930A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1149 removed outlier: 3.671A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1026 through 1029 Processing helix chain 'C' and resid 1057 through 1066 Processing helix chain 'C' and resid 1079 through 1084 Processing helix chain 'C' and resid 1084 through 1096 removed outlier: 3.556A pdb=" N LYS C1088 " --> pdb=" O ASN C1084 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER C1089 " --> pdb=" O PRO C1085 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP C1090 " --> pdb=" O PHE C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1103 through 1108 removed outlier: 4.201A pdb=" N ALA C1108 " --> pdb=" O ALA C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1126 Processing helix chain 'C' and resid 1130 through 1150 removed outlier: 3.827A pdb=" N CYS C1134 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1169 removed outlier: 4.137A pdb=" N TYR C1168 " --> pdb=" O PHE C1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C1169 " --> pdb=" O CYS C1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1164 through 1169' Processing helix chain 'D' and resid 1026 through 1029 Processing helix chain 'D' and resid 1057 through 1065 Processing helix chain 'D' and resid 1079 through 1084 Processing helix chain 'D' and resid 1087 through 1096 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1103 through 1108 removed outlier: 3.807A pdb=" N ALA D1108 " --> pdb=" O ALA D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1111 through 1124 removed outlier: 4.416A pdb=" N TYR D1115 " --> pdb=" O GLU D1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1150 removed outlier: 3.679A pdb=" N TYR D1142 " --> pdb=" O ALA D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 3.535A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.924A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1179 removed outlier: 3.733A pdb=" N GLY A1205 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 3.568A pdb=" N GLN A1223 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 918 through 919 removed outlier: 4.197A pdb=" N ALA B 901 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP B1014 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 984 removed outlier: 3.534A pdb=" N SER B 976 " --> pdb=" O LYS B 979 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU B 972 " --> pdb=" O ILE B 983 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1176 through 1178 Processing sheet with id=AA8, first strand: chain 'B' and resid 1216 through 1217 Processing sheet with id=AA9, first strand: chain 'C' and resid 918 through 920 Processing sheet with id=AB1, first strand: chain 'C' and resid 926 through 931 removed outlier: 6.790A pdb=" N VAL C 946 " --> pdb=" O LEU C 929 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN C 931 " --> pdb=" O PHE C 944 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE C 944 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 963 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL C 951 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 961 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 966 " --> pdb=" O LEU C 973 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU C 972 " --> pdb=" O ILE C 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1048 through 1049 Processing sheet with id=AB3, first strand: chain 'C' and resid 1176 through 1179 removed outlier: 3.589A pdb=" N GLY C1205 " --> pdb=" O GLN C1179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1216 through 1217 Processing sheet with id=AB5, first strand: chain 'D' and resid 918 through 920 removed outlier: 3.982A pdb=" N LEU D1010 " --> pdb=" O THR D1006 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP D1014 " --> pdb=" O LEU D1002 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 926 through 931 removed outlier: 5.941A pdb=" N GLU D 926 " --> pdb=" O ASN D 950 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASN D 950 " --> pdb=" O GLU D 926 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 928 " --> pdb=" O THR D 948 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR D 948 " --> pdb=" O THR D 928 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL D 930 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 951 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER D 961 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU D 972 " --> pdb=" O ILE D 983 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1176 through 1179 removed outlier: 3.721A pdb=" N GLY D1205 " --> pdb=" O GLN D1179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1216 through 1218 removed outlier: 3.571A pdb=" N GLN D1223 " --> pdb=" O ASP D1218 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3392 1.35 - 1.46: 2495 1.46 - 1.58: 4420 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 10443 Sorted by residual: bond pdb=" N GLN C 989 " pdb=" CA GLN C 989 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.83e+00 bond pdb=" CA CYS D1161 " pdb=" CB CYS D1161 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.08e+00 bond pdb=" CA CYS D1161 " pdb=" C CYS D1161 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.20e-01 bond pdb=" N THR B1018 " pdb=" CA THR B1018 " ideal model delta sigma weight residual 1.460 1.473 -0.013 1.54e-02 4.22e+03 7.44e-01 bond pdb=" N THR C1018 " pdb=" CA THR C1018 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 6.12e-01 ... (remaining 10438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 13845 1.24 - 2.48: 269 2.48 - 3.72: 86 3.72 - 4.96: 12 4.96 - 6.20: 3 Bond angle restraints: 14215 Sorted by residual: angle pdb=" C GLN C 989 " pdb=" CA GLN C 989 " pdb=" CB GLN C 989 " ideal model delta sigma weight residual 110.42 116.11 -5.69 1.99e+00 2.53e-01 8.18e+00 angle pdb=" C SER A 939 " pdb=" N THR A 940 " pdb=" CA THR A 940 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.23e+00 angle pdb=" CA GLY B1182 " pdb=" C GLY B1182 " pdb=" O GLY B1182 " ideal model delta sigma weight residual 122.39 120.11 2.28 9.30e-01 1.16e+00 6.03e+00 angle pdb=" CA CYS A1126 " pdb=" CB CYS A1126 " pdb=" SG CYS A1126 " ideal model delta sigma weight residual 114.40 120.04 -5.64 2.30e+00 1.89e-01 6.02e+00 angle pdb=" C ASP A1199 " pdb=" N VAL A1200 " pdb=" CA VAL A1200 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.79e+00 ... (remaining 14210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 5549 18.10 - 36.20: 608 36.20 - 54.30: 135 54.30 - 72.40: 18 72.40 - 90.50: 17 Dihedral angle restraints: 6327 sinusoidal: 2512 harmonic: 3815 Sorted by residual: dihedral pdb=" CB CYS A 953 " pdb=" SG CYS A 953 " pdb=" SG CYS A 960 " pdb=" CB CYS A 960 " ideal model delta sinusoidal sigma weight residual 93.00 -176.50 -90.50 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C1126 " pdb=" SG CYS C1126 " pdb=" SG CYS C1134 " pdb=" CB CYS C1134 " ideal model delta sinusoidal sigma weight residual -86.00 -174.87 88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS C1152 " pdb=" SG CYS C1152 " pdb=" SG CYS C1181 " pdb=" CB CYS C1181 " ideal model delta sinusoidal sigma weight residual -86.00 -163.23 77.23 1 1.00e+01 1.00e-02 7.48e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 955 0.029 - 0.058: 341 0.058 - 0.088: 101 0.088 - 0.117: 111 0.117 - 0.146: 13 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA VAL C1200 " pdb=" N VAL C1200 " pdb=" C VAL C1200 " pdb=" CB VAL C1200 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA THR A1018 " pdb=" N THR A1018 " pdb=" C THR A1018 " pdb=" CB THR A1018 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL A 905 " pdb=" N VAL A 905 " pdb=" C VAL A 905 " pdb=" CB VAL A 905 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1518 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D1191 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO D1192 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D1192 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D1192 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C1211 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO C1212 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C1212 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C1212 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1111 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A1112 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A1112 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1112 " 0.017 5.00e-02 4.00e+02 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1131 2.75 - 3.29: 11011 3.29 - 3.82: 18086 3.82 - 4.36: 20219 4.36 - 4.90: 33741 Nonbonded interactions: 84188 Sorted by model distance: nonbonded pdb=" OD1 ASN D1045 " pdb="CA CA D1401 " model vdw 2.209 3.250 nonbonded pdb=" OD1 ASN D1038 " pdb="CA CA D1401 " model vdw 2.218 3.250 nonbonded pdb=" OD1 ASN A1038 " pdb="CA CA A1401 " model vdw 2.229 3.250 nonbonded pdb=" OD1 ASP B1040 " pdb="CA CA B1401 " model vdw 2.240 3.250 nonbonded pdb=" OG SER D1025 " pdb=" OE1 GLU D1027 " model vdw 2.241 3.040 ... (remaining 84183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 899 through 1401) selection = chain 'C' selection = (chain 'D' and resid 899 through 1401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10501 Z= 0.106 Angle : 0.489 6.199 14331 Z= 0.262 Chirality : 0.042 0.146 1521 Planarity : 0.003 0.039 1886 Dihedral : 14.955 83.588 3719 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 23.02 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1325 helix: 1.47 (0.32), residues: 263 sheet: -0.20 (0.35), residues: 252 loop : -0.60 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1031 TYR 0.008 0.001 TYR C1142 PHE 0.012 0.001 PHE C 944 TRP 0.008 0.001 TRP B1155 HIS 0.002 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (10443) covalent geometry : angle 0.48721 / 0.26 (14215) SS BOND : bond 0.00250 / 0.18 ( 58) SS BOND : angle 0.69046 / 0.51 ( 116) hydrogen bonds : bond 0.21908 / 15.14 ( 366) hydrogen bonds : angle 8.39040 / 6.04 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8449 (t0) cc_final: 0.8126 (t0) REVERT: B 998 MET cc_start: 0.9120 (mmm) cc_final: 0.8770 (mmp) REVERT: C 1187 ARG cc_start: 0.9244 (ptt180) cc_final: 0.8691 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1863 time to fit residues: 10.9818 Evaluate side-chains 29 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 917 GLN B1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.034578 restraints weight = 56864.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036174 restraints weight = 31735.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037284 restraints weight = 22245.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038043 restraints weight = 17640.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038566 restraints weight = 15107.292| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10501 Z= 0.190 Angle : 0.573 5.992 14331 Z= 0.306 Chirality : 0.045 0.163 1521 Planarity : 0.004 0.063 1886 Dihedral : 4.076 21.015 1429 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.49 % Allowed : 22.04 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.24), residues: 1325 helix: 1.43 (0.31), residues: 264 sheet: -0.02 (0.35), residues: 249 loop : -0.59 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1193 TYR 0.016 0.001 TYR D1167 PHE 0.010 0.001 PHE C 944 TRP 0.008 0.001 TRP A1014 HIS 0.008 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (10443) covalent geometry : angle 0.57025 / 0.31 (14215) SS BOND : bond 0.00406 / 0.32 ( 58) SS BOND : angle 0.83834 / 0.57 ( 116) hydrogen bonds : bond 0.04822 / 3.30 ( 366) hydrogen bonds : angle 6.11205 / 4.35 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 33 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8833 (tptm) REVERT: B 998 MET cc_start: 0.9129 (mmm) cc_final: 0.8789 (mmp) REVERT: B 1019 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 1216 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8822 (mm) outliers start: 28 outliers final: 17 residues processed: 58 average time/residue: 0.1165 time to fit residues: 9.7304 Evaluate side-chains 51 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1210 CYS Chi-restraints excluded: chain C residue 1216 ILE Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 125 optimal weight: 0.0470 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 996 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.049453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.035693 restraints weight = 56425.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037311 restraints weight = 31463.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038452 restraints weight = 21834.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.039236 restraints weight = 17239.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039772 restraints weight = 14661.488| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10501 Z= 0.116 Angle : 0.538 8.402 14331 Z= 0.284 Chirality : 0.045 0.156 1521 Planarity : 0.004 0.037 1886 Dihedral : 3.960 16.302 1429 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.93 % Allowed : 20.62 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1325 helix: 1.39 (0.31), residues: 264 sheet: 0.34 (0.35), residues: 245 loop : -0.65 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1193 TYR 0.013 0.001 TYR D1167 PHE 0.011 0.001 PHE C 967 TRP 0.009 0.001 TRP D1065 HIS 0.005 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (10443) covalent geometry : angle 0.52939 / 0.28 (14215) SS BOND : bond 0.00368 / 0.28 ( 58) SS BOND : angle 1.18803 / 0.83 ( 116) hydrogen bonds : bond 0.03951 / 2.68 ( 366) hydrogen bonds : angle 5.53449 / 3.92 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 33 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1088 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9177 (tppt) REVERT: B 996 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: B 998 MET cc_start: 0.9168 (mmm) cc_final: 0.8779 (mmp) REVERT: B 1019 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8589 (p) REVERT: D 998 MET cc_start: 0.9266 (tpp) cc_final: 0.8909 (tpt) outliers start: 33 outliers final: 18 residues processed: 64 average time/residue: 0.1100 time to fit residues: 10.1302 Evaluate side-chains 50 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 29 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1193 ARG Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.034653 restraints weight = 58193.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.036231 restraints weight = 32674.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037329 restraints weight = 22813.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038077 restraints weight = 18090.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038607 restraints weight = 15493.432| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10501 Z= 0.181 Angle : 0.553 6.664 14331 Z= 0.291 Chirality : 0.044 0.151 1521 Planarity : 0.004 0.048 1886 Dihedral : 4.038 17.408 1429 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.64 % Allowed : 20.71 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1325 helix: 1.33 (0.31), residues: 266 sheet: 0.47 (0.35), residues: 246 loop : -0.67 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1198 TYR 0.010 0.001 TYR C 911 PHE 0.009 0.001 PHE C1061 TRP 0.008 0.001 TRP A1014 HIS 0.006 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (10443) covalent geometry : angle 0.54652 / 0.29 (14215) SS BOND : bond 0.00290 / 0.21 ( 58) SS BOND : angle 1.10606 / 0.68 ( 116) hydrogen bonds : bond 0.03857 / 2.67 ( 366) hydrogen bonds : angle 5.41999 / 3.84 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 29 time to evaluate : 0.431 Fit side-chains REVERT: A 974 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8786 (tptm) REVERT: A 1088 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9214 (tppt) REVERT: B 998 MET cc_start: 0.9201 (mmm) cc_final: 0.8809 (mmp) REVERT: B 1019 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 1193 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8519 (mtp-110) outliers start: 41 outliers final: 23 residues processed: 68 average time/residue: 0.1147 time to fit residues: 11.1638 Evaluate side-chains 51 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 25 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1186 LEU Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.048972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035248 restraints weight = 56703.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036829 restraints weight = 31671.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037933 restraints weight = 22141.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038667 restraints weight = 17564.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.039205 restraints weight = 15084.023| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10501 Z= 0.119 Angle : 0.548 9.678 14331 Z= 0.284 Chirality : 0.044 0.249 1521 Planarity : 0.004 0.038 1886 Dihedral : 3.951 17.889 1429 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.58 % Allowed : 21.69 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1325 helix: 1.26 (0.31), residues: 266 sheet: 0.32 (0.35), residues: 245 loop : -0.63 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1050 TYR 0.010 0.001 TYR D1167 PHE 0.011 0.001 PHE C 967 TRP 0.010 0.001 TRP B1065 HIS 0.004 0.000 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10443) covalent geometry : angle 0.54398 / 0.28 (14215) SS BOND : bond 0.00384 / 0.30 ( 58) SS BOND : angle 0.89331 / 0.58 ( 116) hydrogen bonds : bond 0.03489 / 2.42 ( 366) hydrogen bonds : angle 5.16337 / 3.65 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 28 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: B 998 MET cc_start: 0.9222 (mmm) cc_final: 0.8794 (mmp) REVERT: B 1019 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8582 (p) REVERT: D 1193 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8492 (mtp-110) outliers start: 29 outliers final: 21 residues processed: 56 average time/residue: 0.0924 time to fit residues: 8.0276 Evaluate side-chains 45 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 23 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1193 ARG Chi-restraints excluded: chain C residue 1210 CYS Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1023 ASN D1063 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035364 restraints weight = 57292.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036983 restraints weight = 31862.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.038088 restraints weight = 22238.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038846 restraints weight = 17592.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039382 restraints weight = 15092.945| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10501 Z= 0.114 Angle : 0.529 8.978 14331 Z= 0.271 Chirality : 0.044 0.157 1521 Planarity : 0.003 0.038 1886 Dihedral : 3.898 17.314 1429 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.47 % Allowed : 21.33 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1325 helix: 1.30 (0.31), residues: 266 sheet: 0.42 (0.34), residues: 247 loop : -0.68 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1050 TYR 0.012 0.001 TYR D1167 PHE 0.009 0.001 PHE C 967 TRP 0.007 0.001 TRP D1065 HIS 0.003 0.000 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10443) covalent geometry : angle 0.52670 / 0.27 (14215) SS BOND : bond 0.00234 / 0.17 ( 58) SS BOND : angle 0.72664 / 0.51 ( 116) hydrogen bonds : bond 0.03342 / 2.32 ( 366) hydrogen bonds : angle 4.96030 / 3.52 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 28 time to evaluate : 0.451 Fit side-chains REVERT: A 974 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8768 (tptm) REVERT: B 998 MET cc_start: 0.9232 (mmm) cc_final: 0.8801 (mmp) REVERT: B 1019 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 1122 ASP cc_start: 0.9198 (m-30) cc_final: 0.8867 (p0) REVERT: D 1193 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8503 (mtp-110) outliers start: 39 outliers final: 24 residues processed: 64 average time/residue: 0.0904 time to fit residues: 8.9578 Evaluate side-chains 52 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 26 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.048672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.035020 restraints weight = 57542.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036607 restraints weight = 32038.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037686 restraints weight = 22392.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.038452 restraints weight = 17736.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038969 restraints weight = 15150.930| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10501 Z= 0.161 Angle : 0.547 7.539 14331 Z= 0.282 Chirality : 0.044 0.184 1521 Planarity : 0.003 0.037 1886 Dihedral : 4.071 30.947 1429 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.02 % Allowed : 22.31 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1325 helix: 1.36 (0.31), residues: 266 sheet: 0.46 (0.34), residues: 246 loop : -0.62 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1050 TYR 0.011 0.001 TYR D1167 PHE 0.010 0.001 PHE C1061 TRP 0.008 0.001 TRP A1014 HIS 0.004 0.001 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10443) covalent geometry : angle 0.54401 / 0.28 (14215) SS BOND : bond 0.00258 / 0.19 ( 58) SS BOND : angle 0.83514 / 0.54 ( 116) hydrogen bonds : bond 0.03471 / 2.42 ( 366) hydrogen bonds : angle 4.95176 / 3.50 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 26 time to evaluate : 0.388 Fit side-chains REVERT: A 974 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8784 (tptm) REVERT: B 998 MET cc_start: 0.9234 (mmm) cc_final: 0.8831 (mmp) REVERT: B 1019 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8585 (p) REVERT: D 1122 ASP cc_start: 0.9127 (m-30) cc_final: 0.8871 (p0) REVERT: D 1193 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8495 (mtp-110) outliers start: 34 outliers final: 27 residues processed: 57 average time/residue: 0.0854 time to fit residues: 7.7672 Evaluate side-chains 53 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 24 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1015 ASP Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 2.9990 chunk 75 optimal weight: 0.0040 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 69 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035697 restraints weight = 55437.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037308 restraints weight = 30994.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038443 restraints weight = 21675.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.039234 restraints weight = 17136.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039753 restraints weight = 14619.677| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10501 Z= 0.098 Angle : 0.533 6.946 14331 Z= 0.272 Chirality : 0.044 0.218 1521 Planarity : 0.004 0.041 1886 Dihedral : 3.943 24.918 1429 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.76 % Allowed : 22.58 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1325 helix: 1.23 (0.31), residues: 266 sheet: -0.02 (0.33), residues: 269 loop : -0.59 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1050 TYR 0.013 0.001 TYR D1167 PHE 0.011 0.001 PHE C 967 TRP 0.007 0.001 TRP D1065 HIS 0.002 0.000 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (10443) covalent geometry : angle 0.53022 / 0.27 (14215) SS BOND : bond 0.00232 / 0.17 ( 58) SS BOND : angle 0.82458 / 0.54 ( 116) hydrogen bonds : bond 0.03117 / 2.16 ( 366) hydrogen bonds : angle 4.78725 / 3.40 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.412 Fit side-chains REVERT: A 974 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8782 (tptm) REVERT: B 998 MET cc_start: 0.9235 (mmm) cc_final: 0.8777 (mmp) REVERT: B 1019 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8552 (p) REVERT: D 1193 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8582 (mtp-110) outliers start: 31 outliers final: 24 residues processed: 61 average time/residue: 0.0770 time to fit residues: 7.8508 Evaluate side-chains 54 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 28 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1020 ILE Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035408 restraints weight = 56549.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037013 restraints weight = 31673.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038110 restraints weight = 22172.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038890 restraints weight = 17587.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039401 restraints weight = 15023.668| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10501 Z= 0.113 Angle : 0.530 10.645 14331 Z= 0.268 Chirality : 0.044 0.198 1521 Planarity : 0.003 0.040 1886 Dihedral : 3.818 17.295 1429 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.58 % Allowed : 22.93 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1325 helix: 1.30 (0.31), residues: 264 sheet: 0.20 (0.34), residues: 267 loop : -0.62 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1050 TYR 0.011 0.001 TYR D1167 PHE 0.008 0.001 PHE C 967 TRP 0.007 0.001 TRP A1014 HIS 0.003 0.000 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10443) covalent geometry : angle 0.52781 / 0.27 (14215) SS BOND : bond 0.00243 / 0.17 ( 58) SS BOND : angle 0.74480 / 0.52 ( 116) hydrogen bonds : bond 0.03157 / 2.19 ( 366) hydrogen bonds : angle 4.76200 / 3.37 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 28 time to evaluate : 0.416 Fit side-chains REVERT: A 974 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8793 (tptm) REVERT: B 998 MET cc_start: 0.9222 (mmm) cc_final: 0.8785 (mmp) REVERT: B 1019 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (p) REVERT: D 998 MET cc_start: 0.9254 (tpp) cc_final: 0.8893 (tpt) REVERT: D 1193 ARG cc_start: 0.8814 (mtp-110) cc_final: 0.8532 (mtp-110) outliers start: 29 outliers final: 27 residues processed: 54 average time/residue: 0.0775 time to fit residues: 7.0699 Evaluate side-chains 56 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1186 LEU Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 125 optimal weight: 0.0030 chunk 124 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.049563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035541 restraints weight = 55267.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037150 restraints weight = 31106.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038259 restraints weight = 21818.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.039057 restraints weight = 17276.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039509 restraints weight = 14718.274| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10501 Z= 0.107 Angle : 0.527 10.292 14331 Z= 0.265 Chirality : 0.043 0.185 1521 Planarity : 0.003 0.040 1886 Dihedral : 3.778 17.630 1429 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.58 % Allowed : 23.29 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1325 helix: 1.33 (0.31), residues: 264 sheet: 0.25 (0.34), residues: 267 loop : -0.59 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1050 TYR 0.014 0.001 TYR D1167 PHE 0.008 0.001 PHE C 967 TRP 0.006 0.001 TRP A1014 HIS 0.003 0.000 HIS D 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10443) covalent geometry : angle 0.52505 / 0.26 (14215) SS BOND : bond 0.00231 / 0.16 ( 58) SS BOND : angle 0.69572 / 0.49 ( 116) hydrogen bonds : bond 0.03110 / 2.16 ( 366) hydrogen bonds : angle 4.67054 / 3.30 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 26 time to evaluate : 0.401 Fit side-chains REVERT: A 974 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8796 (tptm) REVERT: B 998 MET cc_start: 0.9213 (mmm) cc_final: 0.8758 (mmp) REVERT: B 1019 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 998 MET cc_start: 0.9264 (tpp) cc_final: 0.8872 (tpt) REVERT: D 1041 ASP cc_start: 0.8736 (p0) cc_final: 0.8523 (p0) REVERT: D 1193 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8506 (mtp-110) outliers start: 29 outliers final: 27 residues processed: 53 average time/residue: 0.0785 time to fit residues: 6.9335 Evaluate side-chains 55 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 26 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.049344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.035453 restraints weight = 56543.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037075 restraints weight = 31435.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.038195 restraints weight = 21906.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038985 restraints weight = 17267.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039535 restraints weight = 14695.081| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10501 Z= 0.120 Angle : 0.527 9.883 14331 Z= 0.265 Chirality : 0.043 0.166 1521 Planarity : 0.003 0.040 1886 Dihedral : 3.786 17.340 1429 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.76 % Allowed : 23.11 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1325 helix: 1.32 (0.31), residues: 266 sheet: 0.36 (0.35), residues: 257 loop : -0.56 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1050 TYR 0.013 0.001 TYR D1167 PHE 0.008 0.001 PHE C1061 TRP 0.006 0.001 TRP A1014 HIS 0.003 0.000 HIS C 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10443) covalent geometry : angle 0.52496 / 0.26 (14215) SS BOND : bond 0.00237 / 0.17 ( 58) SS BOND : angle 0.69874 / 0.50 ( 116) hydrogen bonds : bond 0.03151 / 2.19 ( 366) hydrogen bonds : angle 4.65619 / 3.29 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.53 seconds wall clock time: 32 minutes 36.41 seconds (1956.41 seconds total)