Starting phenix.real_space_refine on Thu May 1 08:11:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsp_18638/05_2025/8qsp_18638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsp_18638/05_2025/8qsp_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_18638/05_2025/8qsp_18638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsp_18638/05_2025/8qsp_18638.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsp_18638/05_2025/8qsp_18638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsp_18638/05_2025/8qsp_18638.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.17, per 1000 atoms: 0.80 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: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.54 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: 3.83 Time building geometry restraints manager: 3.34 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 2.510 nonbonded pdb=" OD1 ASN D1038 " pdb="CA CA D1401 " model vdw 2.218 2.510 nonbonded pdb=" OD1 ASN A1038 " pdb="CA CA A1401 " model vdw 2.229 2.510 nonbonded pdb=" OD1 ASP B1040 " pdb="CA CA B1401 " model vdw 2.240 2.510 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 1229 or resid 1401)) selection = chain 'C' selection = (chain 'D' and (resid 899 through 1229 or resid 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: 9.600 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.220 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP B1155 HIS 0.002 0.001 HIS C 910 PHE 0.012 0.001 PHE C 944 TYR 0.008 0.001 TYR C1142 ARG 0.001 0.000 ARG B1031 Details of bonding type rmsd hydrogen bonds : bond 0.21908 ( 366) hydrogen bonds : angle 8.39040 ( 984) SS BOND : bond 0.00250 ( 58) SS BOND : angle 0.69046 ( 116) covalent geometry : bond 0.00219 (10443) covalent geometry : angle 0.48721 (14215) *********************** 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 : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.8455 (ptp90) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.4058 time to fit residues: 24.1254 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 : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 0.0010 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035318 restraints weight = 55739.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036923 restraints weight = 31212.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.038015 restraints weight = 21875.239| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0981 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= 0.137 Angle : 0.547 6.309 14331 Z= 0.291 Chirality : 0.045 0.167 1521 Planarity : 0.004 0.060 1886 Dihedral : 3.956 21.879 1429 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.13 % Allowed : 21.78 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1325 helix: 1.39 (0.31), residues: 264 sheet: 0.02 (0.35), residues: 249 loop : -0.57 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1155 HIS 0.007 0.001 HIS C 910 PHE 0.011 0.001 PHE C 944 TYR 0.018 0.001 TYR D1167 ARG 0.006 0.001 ARG C1193 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 366) hydrogen bonds : angle 5.99938 ( 984) SS BOND : bond 0.00292 ( 58) SS BOND : angle 0.80682 ( 116) covalent geometry : bond 0.00289 (10443) covalent geometry : angle 0.54438 (14215) *********************** 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 58 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8497 (t0) cc_final: 0.8156 (t0) REVERT: B 998 MET cc_start: 0.9145 (mmm) cc_final: 0.8777 (mmp) REVERT: B 1019 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8653 (p) REVERT: C 1216 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.8808 (mm) outliers start: 24 outliers final: 14 residues processed: 55 average time/residue: 0.2792 time to fit residues: 22.2538 Evaluate side-chains 47 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1024 LEU 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 930 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 96 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.049168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035520 restraints weight = 56053.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037114 restraints weight = 31233.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038256 restraints weight = 21734.413| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10501 Z= 0.130 Angle : 0.533 9.253 14331 Z= 0.282 Chirality : 0.044 0.161 1521 Planarity : 0.004 0.036 1886 Dihedral : 3.928 17.598 1429 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.20 % Allowed : 19.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1325 helix: 1.34 (0.31), residues: 264 sheet: -0.00 (0.34), residues: 264 loop : -0.57 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1065 HIS 0.005 0.001 HIS C 910 PHE 0.010 0.001 PHE C 967 TYR 0.012 0.001 TYR D1167 ARG 0.005 0.000 ARG C1193 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 366) hydrogen bonds : angle 5.53386 ( 984) SS BOND : bond 0.00261 ( 58) SS BOND : angle 1.25352 ( 116) covalent geometry : bond 0.00290 (10443) covalent geometry : angle 0.52281 (14215) *********************** 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 68 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 32 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8822 (tptm) REVERT: A 1221 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9374 (tptp) REVERT: B 998 MET cc_start: 0.9167 (mmm) cc_final: 0.8782 (mmp) REVERT: B 1019 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8626 (p) REVERT: D 998 MET cc_start: 0.9234 (tpp) cc_final: 0.8900 (tpt) outliers start: 36 outliers final: 22 residues processed: 66 average time/residue: 0.2405 time to fit residues: 23.8928 Evaluate side-chains 54 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 29 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 1004 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1221 LYS 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 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 1157 THR Chi-restraints excluded: chain C residue 1181 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.0470 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.049571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.035656 restraints weight = 55959.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037275 restraints weight = 31581.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.038379 restraints weight = 22141.916| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10501 Z= 0.107 Angle : 0.517 6.348 14331 Z= 0.269 Chirality : 0.044 0.148 1521 Planarity : 0.004 0.036 1886 Dihedral : 3.863 17.484 1429 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.84 % Allowed : 21.07 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1325 helix: 1.32 (0.31), residues: 264 sheet: -0.00 (0.34), residues: 265 loop : -0.55 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1065 HIS 0.003 0.000 HIS C 910 PHE 0.010 0.001 PHE C 967 TYR 0.009 0.001 TYR D1167 ARG 0.003 0.000 ARG C1198 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 366) hydrogen bonds : angle 5.21872 ( 984) SS BOND : bond 0.00240 ( 58) SS BOND : angle 0.96680 ( 116) covalent geometry : bond 0.00242 (10443) covalent geometry : angle 0.51154 (14215) *********************** 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 64 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 32 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8777 (tptm) REVERT: A 1088 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9169 (tppt) REVERT: B 998 MET cc_start: 0.9181 (mmm) cc_final: 0.8898 (mmm) REVERT: B 1019 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 1122 ASP cc_start: 0.9219 (m-30) cc_final: 0.8876 (p0) outliers start: 32 outliers final: 20 residues processed: 62 average time/residue: 0.2761 time to fit residues: 24.2737 Evaluate side-chains 48 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 1088 LYS 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 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1036 CYS 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 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 15 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 41 optimal weight: 0.0170 chunk 21 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3246 r_free = 0.3246 target = 0.049881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035981 restraints weight = 55591.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.037598 restraints weight = 31176.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038741 restraints weight = 21763.035| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10501 Z= 0.097 Angle : 0.527 8.052 14331 Z= 0.271 Chirality : 0.044 0.267 1521 Planarity : 0.003 0.039 1886 Dihedral : 3.770 17.218 1429 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.38 % Allowed : 20.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1325 helix: 1.27 (0.31), residues: 264 sheet: 0.03 (0.34), residues: 265 loop : -0.57 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D1065 HIS 0.002 0.000 HIS C 910 PHE 0.010 0.001 PHE C 967 TYR 0.011 0.001 TYR B1001 ARG 0.002 0.000 ARG B1052 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 366) hydrogen bonds : angle 5.01948 ( 984) SS BOND : bond 0.00232 ( 58) SS BOND : angle 0.78111 ( 116) covalent geometry : bond 0.00223 (10443) covalent geometry : angle 0.52486 (14215) *********************** 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 69 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 31 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8770 (tptm) REVERT: B 1019 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 998 MET cc_start: 0.9229 (tpp) cc_final: 0.8762 (tpt) REVERT: D 1122 ASP cc_start: 0.9221 (m-30) cc_final: 0.8891 (p0) outliers start: 38 outliers final: 23 residues processed: 65 average time/residue: 0.2056 time to fit residues: 20.7558 Evaluate side-chains 54 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 29 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 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 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 1020 ILE Chi-restraints excluded: chain C residue 1036 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035258 restraints weight = 56251.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036851 restraints weight = 31580.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037963 restraints weight = 22060.984| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10501 Z= 0.151 Angle : 0.538 7.687 14331 Z= 0.276 Chirality : 0.044 0.250 1521 Planarity : 0.003 0.038 1886 Dihedral : 3.847 16.394 1429 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.56 % Allowed : 20.44 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1325 helix: 1.34 (0.31), residues: 266 sheet: 0.18 (0.34), residues: 267 loop : -0.56 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1014 HIS 0.004 0.001 HIS C 910 PHE 0.009 0.001 PHE C1061 TYR 0.012 0.001 TYR D1167 ARG 0.004 0.000 ARG C1198 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 366) hydrogen bonds : angle 4.97232 ( 984) SS BOND : bond 0.00342 ( 58) SS BOND : angle 0.84243 ( 116) covalent geometry : bond 0.00334 (10443) covalent geometry : angle 0.53507 (14215) *********************** 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 69 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 29 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8805 (tptm) REVERT: B 998 MET cc_start: 0.9198 (mmm) cc_final: 0.8790 (mmp) REVERT: B 1019 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 1122 ASP cc_start: 0.9153 (m-30) cc_final: 0.8924 (p0) outliers start: 40 outliers final: 28 residues processed: 68 average time/residue: 0.2025 time to fit residues: 21.2487 Evaluate side-chains 58 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 28 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 1024 LEU Chi-restraints excluded: chain A residue 1082 THR 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 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 1012 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.048999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.035103 restraints weight = 56561.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.036695 restraints weight = 31802.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037811 restraints weight = 22230.363| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10501 Z= 0.146 Angle : 0.536 6.687 14331 Z= 0.276 Chirality : 0.044 0.204 1521 Planarity : 0.004 0.037 1886 Dihedral : 4.027 32.640 1429 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.29 % Allowed : 21.07 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1325 helix: 1.33 (0.31), residues: 266 sheet: 0.20 (0.34), residues: 266 loop : -0.50 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1014 HIS 0.004 0.001 HIS C 910 PHE 0.010 0.001 PHE C1061 TYR 0.013 0.001 TYR D1167 ARG 0.003 0.000 ARG C1187 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 366) hydrogen bonds : angle 4.90796 ( 984) SS BOND : bond 0.00276 ( 58) SS BOND : angle 0.80914 ( 116) covalent geometry : bond 0.00324 (10443) covalent geometry : angle 0.53288 (14215) *********************** 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 64 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 27 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8811 (tptm) REVERT: A 1088 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9195 (tppt) REVERT: B 998 MET cc_start: 0.9182 (mmm) cc_final: 0.8780 (mmp) REVERT: B 1019 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8632 (p) REVERT: D 1122 ASP cc_start: 0.9157 (m-30) cc_final: 0.8939 (p0) outliers start: 37 outliers final: 27 residues processed: 62 average time/residue: 0.2434 time to fit residues: 22.8787 Evaluate side-chains 54 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 24 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 1082 THR Chi-restraints excluded: chain A residue 1088 LYS 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 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 1012 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035296 restraints weight = 56669.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036874 restraints weight = 31670.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037989 restraints weight = 22091.982| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10501 Z= 0.150 Angle : 0.534 7.463 14331 Z= 0.275 Chirality : 0.044 0.195 1521 Planarity : 0.003 0.037 1886 Dihedral : 3.972 24.000 1429 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.93 % Allowed : 21.24 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1325 helix: 1.32 (0.31), residues: 266 sheet: 0.22 (0.34), residues: 266 loop : -0.53 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1014 HIS 0.004 0.001 HIS C 910 PHE 0.009 0.001 PHE C1061 TYR 0.013 0.001 TYR D1167 ARG 0.003 0.000 ARG C1193 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 366) hydrogen bonds : angle 4.86292 ( 984) SS BOND : bond 0.00268 ( 58) SS BOND : angle 0.80554 ( 116) covalent geometry : bond 0.00331 (10443) covalent geometry : angle 0.53114 (14215) *********************** 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 61 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 28 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8813 (tptm) REVERT: A 1088 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9214 (tppt) REVERT: B 998 MET cc_start: 0.9218 (mmm) cc_final: 0.8798 (mmp) REVERT: B 1019 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8667 (p) REVERT: B 1023 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8981 (t0) outliers start: 33 outliers final: 26 residues processed: 59 average time/residue: 0.1938 time to fit residues: 18.1351 Evaluate side-chains 56 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 26 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 1023 ASN 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 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 1012 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.034477 restraints weight = 57441.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.036033 restraints weight = 32728.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037119 restraints weight = 22934.402| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10501 Z= 0.240 Angle : 0.587 7.494 14331 Z= 0.305 Chirality : 0.044 0.188 1521 Planarity : 0.004 0.035 1886 Dihedral : 4.084 17.317 1429 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.29 % Allowed : 21.42 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1325 helix: 1.26 (0.31), residues: 267 sheet: 0.00 (0.33), residues: 288 loop : -0.57 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.006 0.001 HIS C 910 PHE 0.009 0.001 PHE C1061 TYR 0.015 0.001 TYR D1167 ARG 0.004 0.000 ARG C1193 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 366) hydrogen bonds : angle 5.04227 ( 984) SS BOND : bond 0.00343 ( 58) SS BOND : angle 0.83699 ( 116) covalent geometry : bond 0.00515 (10443) covalent geometry : angle 0.58489 (14215) *********************** 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 64 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 27 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8926 (ttpp) REVERT: A 1088 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9233 (tppt) REVERT: B 998 MET cc_start: 0.9198 (mmm) cc_final: 0.8813 (mmp) REVERT: B 1019 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8669 (p) outliers start: 37 outliers final: 29 residues processed: 62 average time/residue: 0.1848 time to fit residues: 18.2376 Evaluate side-chains 58 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 26 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 932 ASN 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 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 1004 VAL Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1012 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 124 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.049212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035495 restraints weight = 56924.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.037082 restraints weight = 31826.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.038164 restraints weight = 22301.141| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1849 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= 0.121 Angle : 0.544 10.654 14331 Z= 0.276 Chirality : 0.044 0.189 1521 Planarity : 0.003 0.038 1886 Dihedral : 3.939 18.002 1429 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.40 % Allowed : 22.22 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1325 helix: 1.30 (0.31), residues: 266 sheet: 0.18 (0.34), residues: 266 loop : -0.55 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1065 HIS 0.004 0.001 HIS C 910 PHE 0.009 0.001 PHE C 944 TYR 0.019 0.001 TYR D1167 ARG 0.002 0.000 ARG C1193 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 366) hydrogen bonds : angle 4.85644 ( 984) SS BOND : bond 0.00261 ( 58) SS BOND : angle 0.71827 ( 116) covalent geometry : bond 0.00274 (10443) covalent geometry : angle 0.54189 (14215) ********************** 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 53 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 26 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8802 (tptm) REVERT: A 1088 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9206 (tppt) REVERT: B 998 MET cc_start: 0.9179 (mmm) cc_final: 0.8763 (mmp) REVERT: B 1019 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8643 (p) REVERT: D 998 MET cc_start: 0.9262 (tpp) cc_final: 0.8891 (tpt) outliers start: 27 outliers final: 22 residues processed: 52 average time/residue: 0.1723 time to fit residues: 14.8070 Evaluate side-chains 48 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 23 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE 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 1012 LEU Chi-restraints excluded: chain C residue 1036 CYS 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 33 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 chunk 92 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.035354 restraints weight = 55389.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.036974 restraints weight = 31373.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038094 restraints weight = 21897.563| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1937 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= 0.111 Angle : 0.530 10.353 14331 Z= 0.268 Chirality : 0.044 0.181 1521 Planarity : 0.003 0.039 1886 Dihedral : 3.819 17.792 1429 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.31 % Allowed : 22.58 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1325 helix: 1.37 (0.31), residues: 260 sheet: 0.17 (0.34), residues: 267 loop : -0.52 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1014 HIS 0.005 0.000 HIS D 910 PHE 0.009 0.001 PHE C 967 TYR 0.014 0.001 TYR D1167 ARG 0.002 0.000 ARG C1190 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 366) hydrogen bonds : angle 4.70386 ( 984) SS BOND : bond 0.00236 ( 58) SS BOND : angle 0.67957 ( 116) covalent geometry : bond 0.00256 (10443) covalent geometry : angle 0.52856 (14215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.72 seconds wall clock time: 59 minutes 42.41 seconds (3582.41 seconds total)