Starting phenix.real_space_refine on Sat Aug 23 06:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsp_18638/08_2025/8qsp_18638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsp_18638/08_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_18638/08_2025/8qsp_18638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsp_18638/08_2025/8qsp_18638.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsp_18638/08_2025/8qsp_18638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsp_18638/08_2025/8qsp_18638.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 128 5.16 5 C 6358 2.51 5 N 1727 2.21 5 O 1957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2520 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2560 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 21, 'TRANS': 313} Chain: "C" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2520 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 21, 'TRANS': 309} Chain: "D" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2570 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 21, 'TRANS': 314} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 2.63, per 1000 atoms: 0.26 Number of scatterers: 10174 At special positions: 0 Unit cell: (87.15, 90.47, 162.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 128 16.00 O 1957 8.00 N 1727 7.00 C 6358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=58, symmetry=0 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1071 " distance=2.03 Simple disulfide: pdb=" SG CYS A 934 " - pdb=" SG CYS A1033 " distance=2.03 Simple disulfide: pdb=" SG CYS A 953 " - pdb=" SG CYS A 960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1095 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1146 " distance=2.03 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1134 " distance=2.04 Simple disulfide: pdb=" SG CYS A1136 " - pdb=" SG CYS A1161 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1181 " distance=2.03 Simple disulfide: pdb=" SG CYS A1165 " - pdb=" SG CYS A1206 " distance=2.03 Simple disulfide: pdb=" SG CYS A1174 " - pdb=" SG CYS B1174 " distance=2.02 Simple disulfide: pdb=" SG CYS A1185 " - pdb=" SG CYS A1196 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1071 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B1033 " distance=2.03 Simple disulfide: pdb=" SG CYS B 953 " - pdb=" SG CYS B 960 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1095 " - pdb=" SG CYS B1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1146 " distance=2.03 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1134 " distance=2.04 Simple disulfide: pdb=" SG CYS B1136 " - pdb=" SG CYS B1161 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1165 " - pdb=" SG CYS B1206 " distance=2.03 Simple disulfide: pdb=" SG CYS B1185 " - pdb=" SG CYS B1196 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1210 " - pdb=" SG CYS B1224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C1071 " distance=2.03 Simple disulfide: pdb=" SG CYS C 934 " - pdb=" SG CYS C1033 " distance=2.03 Simple disulfide: pdb=" SG CYS C 953 " - pdb=" SG CYS C 960 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1095 " - pdb=" SG CYS C1119 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1146 " distance=2.03 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1134 " distance=2.03 Simple disulfide: pdb=" SG CYS C1136 " - pdb=" SG CYS C1161 " distance=2.03 Simple disulfide: pdb=" SG CYS C1152 " - pdb=" SG CYS C1181 " distance=2.03 Simple disulfide: pdb=" SG CYS C1165 " - pdb=" SG CYS C1206 " distance=2.03 Simple disulfide: pdb=" SG CYS C1174 " - pdb=" SG CYS D1174 " distance=2.03 Simple disulfide: pdb=" SG CYS C1185 " - pdb=" SG CYS C1196 " distance=2.03 Simple disulfide: pdb=" SG CYS C1189 " - pdb=" SG CYS C1228 " distance=2.03 Simple disulfide: pdb=" SG CYS C1210 " - pdb=" SG CYS C1224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 903 " - pdb=" SG CYS D1036 " distance=2.03 Simple disulfide: pdb=" SG CYS D 925 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 934 " - pdb=" SG CYS D1033 " distance=2.03 Simple disulfide: pdb=" SG CYS D 953 " - pdb=" SG CYS D 960 " distance=2.03 Simple disulfide: pdb=" SG CYS D1081 " - pdb=" SG CYS D1124 " distance=2.03 Simple disulfide: pdb=" SG CYS D1095 " - pdb=" SG CYS D1119 " distance=2.03 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1146 " distance=2.03 Simple disulfide: pdb=" SG CYS D1126 " - pdb=" SG CYS D1134 " distance=2.04 Simple disulfide: pdb=" SG CYS D1136 " - pdb=" SG CYS D1161 " distance=2.03 Simple disulfide: pdb=" SG CYS D1152 " - pdb=" SG CYS D1181 " distance=2.03 Simple disulfide: pdb=" SG CYS D1165 " - pdb=" SG CYS D1206 " distance=2.03 Simple disulfide: pdb=" SG CYS D1185 " - pdb=" SG CYS D1196 " distance=2.03 Simple disulfide: pdb=" SG CYS D1189 " - pdb=" SG CYS D1228 " distance=2.03 Simple disulfide: pdb=" SG CYS D1210 " - pdb=" SG CYS D1224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 374.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 17 sheets defined 25.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1026 through 1029 Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.658A pdb=" N PHE A1047 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.708A pdb=" N TRP A1065 " --> pdb=" O PHE A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1085 through 1096 removed outlier: 4.413A pdb=" N SER A1089 " --> pdb=" O PRO A1085 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP A1090 " --> pdb=" O PHE A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1102 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1103 through 1108 removed outlier: 3.984A pdb=" N ALA A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1125 Processing helix chain 'A' and resid 1130 through 1149 removed outlier: 3.865A pdb=" N VAL A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 3.979A pdb=" N TYR A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1029 Processing helix chain 'B' and resid 1043 through 1048 removed outlier: 3.825A pdb=" N PHE B1047 " --> pdb=" O VAL B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1065 Processing helix chain 'B' and resid 1079 through 1084 Processing helix chain 'B' and resid 1087 through 1100 removed outlier: 4.843A pdb=" N ILE B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU B1098 " --> pdb=" O GLN B1094 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS B1099 " --> pdb=" O CYS B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1110 removed outlier: 3.930A pdb=" N ALA B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1126 Processing helix chain 'B' and resid 1130 through 1149 removed outlier: 3.671A pdb=" N TYR B1142 " --> pdb=" O ALA B1138 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1026 through 1029 Processing helix chain 'C' and resid 1057 through 1066 Processing helix chain 'C' and resid 1079 through 1084 Processing helix chain 'C' and resid 1084 through 1096 removed outlier: 3.556A pdb=" N LYS C1088 " --> pdb=" O ASN C1084 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER C1089 " --> pdb=" O PRO C1085 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TRP C1090 " --> pdb=" O PHE C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1103 through 1108 removed outlier: 4.201A pdb=" N ALA C1108 " --> pdb=" O ALA C1104 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1126 Processing helix chain 'C' and resid 1130 through 1150 removed outlier: 3.827A pdb=" N CYS C1134 " --> pdb=" O GLY C1130 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1169 removed outlier: 4.137A pdb=" N TYR C1168 " --> pdb=" O PHE C1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C1169 " --> pdb=" O CYS C1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1164 through 1169' Processing helix chain 'D' and resid 1026 through 1029 Processing helix chain 'D' and resid 1057 through 1065 Processing helix chain 'D' and resid 1079 through 1084 Processing helix chain 'D' and resid 1087 through 1096 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1103 through 1108 removed outlier: 3.807A pdb=" N ALA D1108 " --> pdb=" O ALA D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1111 through 1124 removed outlier: 4.416A pdb=" N TYR D1115 " --> pdb=" O GLU D1111 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1150 removed outlier: 3.679A pdb=" N TYR D1142 " --> pdb=" O ALA D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1169 Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920 removed outlier: 3.535A pdb=" N TYR A 911 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.924A pdb=" N VAL A 946 " --> pdb=" O LEU A 929 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 931 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 944 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 951 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER A 961 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1179 removed outlier: 3.733A pdb=" N GLY A1205 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 3.568A pdb=" N GLN A1223 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 918 through 919 removed outlier: 4.197A pdb=" N ALA B 901 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP B1014 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 984 removed outlier: 3.534A pdb=" N SER B 976 " --> pdb=" O LYS B 979 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU B 972 " --> pdb=" O ILE B 983 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 961 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B 951 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 963 " --> pdb=" O GLU B 949 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 946 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1176 through 1178 Processing sheet with id=AA8, first strand: chain 'B' and resid 1216 through 1217 Processing sheet with id=AA9, first strand: chain 'C' and resid 918 through 920 Processing sheet with id=AB1, first strand: chain 'C' and resid 926 through 931 removed outlier: 6.790A pdb=" N VAL C 946 " --> pdb=" O LEU C 929 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLN C 931 " --> pdb=" O PHE C 944 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE C 944 " --> pdb=" O GLN C 931 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C 963 " --> pdb=" O GLU C 949 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL C 951 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER C 961 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 966 " --> pdb=" O LEU C 973 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU C 972 " --> pdb=" O ILE C 983 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1048 through 1049 Processing sheet with id=AB3, first strand: chain 'C' and resid 1176 through 1179 removed outlier: 3.589A pdb=" N GLY C1205 " --> pdb=" O GLN C1179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1216 through 1217 Processing sheet with id=AB5, first strand: chain 'D' and resid 918 through 920 removed outlier: 3.982A pdb=" N LEU D1010 " --> pdb=" O THR D1006 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP D1014 " --> pdb=" O LEU D1002 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 926 through 931 removed outlier: 5.941A pdb=" N GLU D 926 " --> pdb=" O ASN D 950 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASN D 950 " --> pdb=" O GLU D 926 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 928 " --> pdb=" O THR D 948 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR D 948 " --> pdb=" O THR D 928 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL D 930 " --> pdb=" O VAL D 946 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL D 951 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER D 961 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU D 972 " --> pdb=" O ILE D 983 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1176 through 1179 removed outlier: 3.721A pdb=" N GLY D1205 " --> pdb=" O GLN D1179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1216 through 1218 removed outlier: 3.571A pdb=" N GLN D1223 " --> pdb=" O ASP D1218 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.21 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 1401) selection = chain 'C' selection = (chain 'D' and resid 899 through 1401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.130 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1325 helix: 1.47 (0.32), residues: 263 sheet: -0.20 (0.35), residues: 252 loop : -0.60 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1031 TYR 0.008 0.001 TYR C1142 PHE 0.012 0.001 PHE C 944 TRP 0.008 0.001 TRP B1155 HIS 0.002 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00219 (10443) covalent geometry : angle 0.48721 (14215) SS BOND : bond 0.00250 ( 58) SS BOND : angle 0.69046 ( 116) hydrogen bonds : bond 0.21908 ( 366) hydrogen bonds : angle 8.39040 ( 984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1122 ASP cc_start: 0.8449 (t0) cc_final: 0.8126 (t0) REVERT: B 998 MET cc_start: 0.9120 (mmm) cc_final: 0.8770 (mmp) REVERT: C 1187 ARG cc_start: 0.9244 (ptt180) cc_final: 0.8691 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2026 time to fit residues: 11.8007 Evaluate side-chains 29 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3202 r_free = 0.3202 target = 0.048396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.034886 restraints weight = 56978.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036471 restraints weight = 31829.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.037572 restraints weight = 22232.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038335 restraints weight = 17572.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038870 restraints weight = 14976.175| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10501 Z= 0.190 Angle : 0.571 6.179 14331 Z= 0.305 Chirality : 0.045 0.164 1521 Planarity : 0.004 0.063 1886 Dihedral : 4.047 20.998 1429 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.49 % Allowed : 21.96 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1325 helix: 1.43 (0.31), residues: 264 sheet: -0.02 (0.35), residues: 249 loop : -0.58 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1193 TYR 0.017 0.001 TYR D1167 PHE 0.010 0.001 PHE C 944 TRP 0.008 0.001 TRP A1014 HIS 0.008 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00405 (10443) covalent geometry : angle 0.56837 (14215) SS BOND : bond 0.00357 ( 58) SS BOND : angle 0.84009 ( 116) hydrogen bonds : bond 0.04874 ( 366) hydrogen bonds : angle 6.10606 ( 984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8832 (tptm) REVERT: B 998 MET cc_start: 0.9119 (mmm) cc_final: 0.8783 (mmp) REVERT: B 1019 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8592 (p) REVERT: C 1216 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8859 (mm) outliers start: 28 outliers final: 17 residues processed: 56 average time/residue: 0.1119 time to fit residues: 8.8759 Evaluate side-chains 49 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1210 CYS Chi-restraints excluded: chain C residue 1216 ILE Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.049032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035159 restraints weight = 56618.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036736 restraints weight = 31767.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037864 restraints weight = 22257.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038626 restraints weight = 17655.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039163 restraints weight = 15103.996| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10501 Z= 0.133 Angle : 0.539 9.611 14331 Z= 0.285 Chirality : 0.044 0.160 1521 Planarity : 0.004 0.037 1886 Dihedral : 3.978 16.276 1429 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.67 % Allowed : 21.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.24), residues: 1325 helix: 1.34 (0.31), residues: 266 sheet: 0.35 (0.35), residues: 244 loop : -0.61 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1193 TYR 0.012 0.001 TYR D1167 PHE 0.010 0.001 PHE C 967 TRP 0.008 0.001 TRP D1065 HIS 0.005 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00297 (10443) covalent geometry : angle 0.52807 (14215) SS BOND : bond 0.00306 ( 58) SS BOND : angle 1.30820 ( 116) hydrogen bonds : bond 0.04084 ( 366) hydrogen bonds : angle 5.57197 ( 984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1088 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9189 (tppt) REVERT: A 1221 LYS cc_start: 0.9594 (OUTLIER) cc_final: 0.9338 (tptp) REVERT: B 998 MET cc_start: 0.9164 (mmm) cc_final: 0.8792 (mmp) REVERT: B 1019 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 1216 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8800 (mm) outliers start: 30 outliers final: 20 residues processed: 62 average time/residue: 0.0986 time to fit residues: 8.9067 Evaluate side-chains 53 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 VAL 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 A residue 1221 LYS Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1157 THR Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.0570 chunk 9 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1094 GLN ** D 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.034073 restraints weight = 59406.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035603 restraints weight = 33544.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036656 restraints weight = 23677.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037381 restraints weight = 18929.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037872 restraints weight = 16302.544| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10501 Z= 0.272 Angle : 0.612 6.258 14331 Z= 0.322 Chirality : 0.045 0.142 1521 Planarity : 0.004 0.049 1886 Dihedral : 4.303 17.937 1429 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 4.36 % Allowed : 21.16 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.24), residues: 1325 helix: 1.19 (0.31), residues: 267 sheet: 0.21 (0.34), residues: 268 loop : -0.73 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1193 TYR 0.013 0.001 TYR C 911 PHE 0.010 0.002 PHE C1061 TRP 0.012 0.001 TRP A1014 HIS 0.007 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00578 (10443) covalent geometry : angle 0.60546 (14215) SS BOND : bond 0.00383 ( 58) SS BOND : angle 1.14520 ( 116) hydrogen bonds : bond 0.04291 ( 366) hydrogen bonds : angle 5.60128 ( 984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 26 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9023 (tptm) REVERT: A 1088 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9236 (tppt) REVERT: B 998 MET cc_start: 0.9209 (mmm) cc_final: 0.8850 (mmp) REVERT: B 1019 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8607 (p) REVERT: D 1193 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8518 (mtp-110) outliers start: 49 outliers final: 33 residues processed: 72 average time/residue: 0.1043 time to fit residues: 10.8838 Evaluate side-chains 59 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 23 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 1011 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 979 LYS Chi-restraints excluded: chain B residue 1007 ASP 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 1157 THR Chi-restraints excluded: chain B residue 1165 CYS 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 968 LEU Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1055 VAL 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 1015 ASP Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN D 922 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.035133 restraints weight = 56654.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.036709 restraints weight = 32312.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037826 restraints weight = 22644.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038574 restraints weight = 17985.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039062 restraints weight = 15441.020| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1524 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= 0.108 Angle : 0.528 6.445 14331 Z= 0.276 Chirality : 0.044 0.158 1521 Planarity : 0.004 0.037 1886 Dihedral : 4.058 18.525 1429 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1325 helix: 1.30 (0.31), residues: 266 sheet: 0.26 (0.35), residues: 244 loop : -0.64 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1193 TYR 0.014 0.001 TYR D1167 PHE 0.012 0.001 PHE C 967 TRP 0.009 0.001 TRP D1065 HIS 0.010 0.001 HIS B 897 Details of bonding type rmsd covalent geometry : bond 0.00242 (10443) covalent geometry : angle 0.52347 (14215) SS BOND : bond 0.00254 ( 58) SS BOND : angle 0.94558 ( 116) hydrogen bonds : bond 0.03560 ( 366) hydrogen bonds : angle 5.23430 ( 984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 29 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8781 (tptm) REVERT: B 998 MET cc_start: 0.9182 (mmm) cc_final: 0.8793 (mmp) REVERT: B 1019 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 1216 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8858 (mm) REVERT: D 1193 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8505 (mtp-110) outliers start: 39 outliers final: 21 residues processed: 66 average time/residue: 0.0947 time to fit residues: 9.1439 Evaluate side-chains 50 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 26 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 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 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 1181 CYS Chi-restraints excluded: chain C residue 1193 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1121 ASN ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1063 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035198 restraints weight = 56982.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036784 restraints weight = 32239.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037916 restraints weight = 22468.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038690 restraints weight = 17744.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039213 restraints weight = 15135.598| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1668 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= 0.115 Angle : 0.517 7.763 14331 Z= 0.267 Chirality : 0.044 0.153 1521 Planarity : 0.003 0.039 1886 Dihedral : 3.922 17.595 1429 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.76 % Allowed : 22.93 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.24), residues: 1325 helix: 1.33 (0.31), residues: 266 sheet: 0.36 (0.35), residues: 247 loop : -0.68 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1193 TYR 0.011 0.001 TYR D1167 PHE 0.010 0.001 PHE C 967 TRP 0.007 0.001 TRP D1065 HIS 0.003 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00260 (10443) covalent geometry : angle 0.51329 (14215) SS BOND : bond 0.00231 ( 58) SS BOND : angle 0.83811 ( 116) hydrogen bonds : bond 0.03374 ( 366) hydrogen bonds : angle 5.05046 ( 984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 26 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8768 (tptm) REVERT: B 1019 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8554 (p) REVERT: D 1122 ASP cc_start: 0.9158 (m-30) cc_final: 0.8901 (p0) REVERT: D 1193 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8524 (mtp-110) outliers start: 31 outliers final: 23 residues processed: 54 average time/residue: 0.0943 time to fit residues: 7.4480 Evaluate side-chains 49 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 24 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 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 982 VAL Chi-restraints excluded: chain C residue 998 MET 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 C residue 1193 ARG Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1023 ASN ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.048440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.034787 restraints weight = 56978.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036347 restraints weight = 31996.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037422 restraints weight = 22464.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038184 restraints weight = 17821.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038707 restraints weight = 15245.714| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10501 Z= 0.169 Angle : 0.537 7.313 14331 Z= 0.279 Chirality : 0.044 0.227 1521 Planarity : 0.004 0.036 1886 Dihedral : 3.986 17.239 1429 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.82 % Allowed : 22.31 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.24), residues: 1325 helix: 1.37 (0.31), residues: 266 sheet: 0.22 (0.33), residues: 268 loop : -0.67 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1193 TYR 0.010 0.001 TYR C 911 PHE 0.009 0.001 PHE C1061 TRP 0.008 0.001 TRP A1014 HIS 0.005 0.001 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00369 (10443) covalent geometry : angle 0.53420 (14215) SS BOND : bond 0.00270 ( 58) SS BOND : angle 0.83480 ( 116) hydrogen bonds : bond 0.03498 ( 366) hydrogen bonds : angle 5.05999 ( 984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 26 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8798 (tptm) REVERT: B 998 MET cc_start: 0.9164 (mmm) cc_final: 0.8810 (mmp) REVERT: B 1019 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8576 (p) REVERT: D 1193 ARG cc_start: 0.8776 (mtp-110) cc_final: 0.8479 (mtp-110) outliers start: 43 outliers final: 31 residues processed: 64 average time/residue: 0.0869 time to fit residues: 8.3873 Evaluate side-chains 56 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 23 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 1011 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 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 C residue 1193 ARG Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1015 ASP Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 0.9980 chunk 75 optimal weight: 0.0010 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.049323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.035505 restraints weight = 55947.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037085 restraints weight = 31726.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038185 restraints weight = 22247.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.038956 restraints weight = 17648.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039373 restraints weight = 15082.041| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10501 Z= 0.113 Angle : 0.530 9.584 14331 Z= 0.270 Chirality : 0.044 0.205 1521 Planarity : 0.003 0.039 1886 Dihedral : 3.941 17.920 1429 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.20 % Allowed : 23.11 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1325 helix: 1.29 (0.31), residues: 266 sheet: 0.05 (0.34), residues: 267 loop : -0.62 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1198 TYR 0.012 0.001 TYR D1167 PHE 0.010 0.001 PHE C 967 TRP 0.007 0.001 TRP D1065 HIS 0.003 0.000 HIS C 910 Details of bonding type rmsd covalent geometry : bond 0.00256 (10443) covalent geometry : angle 0.52594 (14215) SS BOND : bond 0.00262 ( 58) SS BOND : angle 0.86340 ( 116) hydrogen bonds : bond 0.03250 ( 366) hydrogen bonds : angle 4.90875 ( 984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 26 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8796 (tptm) REVERT: B 998 MET cc_start: 0.9172 (mmm) cc_final: 0.8726 (mmp) REVERT: B 1019 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 1216 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8925 (mm) REVERT: D 998 MET cc_start: 0.9241 (tpp) cc_final: 0.8910 (tpt) REVERT: D 1193 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8543 (mtp-110) outliers start: 36 outliers final: 27 residues processed: 60 average time/residue: 0.0847 time to fit residues: 7.6328 Evaluate side-chains 55 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 25 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 1036 CYS Chi-restraints excluded: chain C residue 1055 VAL Chi-restraints excluded: chain C residue 1181 CYS Chi-restraints excluded: chain C residue 1193 ARG Chi-restraints excluded: chain C residue 1216 ILE Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035358 restraints weight = 56495.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036914 restraints weight = 31726.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038013 restraints weight = 22230.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038728 restraints weight = 17638.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039292 restraints weight = 15162.263| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1852 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= 0.123 Angle : 0.525 9.005 14331 Z= 0.268 Chirality : 0.044 0.202 1521 Planarity : 0.003 0.038 1886 Dihedral : 3.906 18.814 1429 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.02 % Allowed : 23.20 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.24), residues: 1325 helix: 1.25 (0.31), residues: 266 sheet: 0.05 (0.34), residues: 267 loop : -0.62 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1198 TYR 0.014 0.001 TYR D1167 PHE 0.009 0.001 PHE C 967 TRP 0.007 0.001 TRP D1155 HIS 0.004 0.001 HIS D 895 Details of bonding type rmsd covalent geometry : bond 0.00278 (10443) covalent geometry : angle 0.52137 (14215) SS BOND : bond 0.00250 ( 58) SS BOND : angle 0.82762 ( 116) hydrogen bonds : bond 0.03257 ( 366) hydrogen bonds : angle 4.87364 ( 984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 25 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 974 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8805 (tptm) REVERT: B 998 MET cc_start: 0.9166 (mmm) cc_final: 0.8730 (mmp) REVERT: B 1019 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (p) REVERT: C 1216 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8930 (mm) REVERT: D 1193 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8523 (mtp-110) outliers start: 34 outliers final: 29 residues processed: 56 average time/residue: 0.0933 time to fit residues: 7.7341 Evaluate side-chains 56 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 1149 VAL Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 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 C residue 1193 ARG Chi-restraints excluded: chain C residue 1216 ILE Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 114 optimal weight: 0.0980 chunk 125 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.049538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.035820 restraints weight = 54730.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037398 restraints weight = 30778.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038511 restraints weight = 21546.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.039274 restraints weight = 17052.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039784 restraints weight = 14577.303| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10501 Z= 0.099 Angle : 0.527 11.104 14331 Z= 0.266 Chirality : 0.044 0.203 1521 Planarity : 0.003 0.039 1886 Dihedral : 3.848 17.642 1429 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.02 % Allowed : 23.20 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1325 helix: 1.27 (0.31), residues: 266 sheet: 0.08 (0.34), residues: 267 loop : -0.61 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1198 TYR 0.013 0.001 TYR D1167 PHE 0.010 0.001 PHE C 967 TRP 0.007 0.001 TRP C1090 HIS 0.004 0.001 HIS D 910 Details of bonding type rmsd covalent geometry : bond 0.00230 (10443) covalent geometry : angle 0.52325 (14215) SS BOND : bond 0.00232 ( 58) SS BOND : angle 0.87806 ( 116) hydrogen bonds : bond 0.03126 ( 366) hydrogen bonds : angle 4.75409 ( 984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 26 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 998 MET cc_start: 0.9200 (mmm) cc_final: 0.8731 (mmp) REVERT: B 1019 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 1122 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8174 (t0) REVERT: C 1216 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8949 (mm) REVERT: D 1193 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8545 (mtp-110) outliers start: 34 outliers final: 28 residues processed: 56 average time/residue: 0.0799 time to fit residues: 6.8032 Evaluate side-chains 56 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 25 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1024 LEU 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 1122 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 THR Chi-restraints excluded: chain B residue 1195 ASP Chi-restraints excluded: chain B residue 1216 ILE Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 982 VAL Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1010 LEU Chi-restraints excluded: chain C residue 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 C residue 1193 ARG Chi-restraints excluded: chain C residue 1216 ILE Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 1004 VAL Chi-restraints excluded: chain D residue 1055 VAL Chi-restraints excluded: chain D residue 1157 THR Chi-restraints excluded: chain D residue 1183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 59 optimal weight: 0.0020 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.049612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.035790 restraints weight = 55498.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.037410 restraints weight = 31109.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038526 restraints weight = 21657.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.039323 restraints weight = 17081.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039887 restraints weight = 14530.711| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10501 Z= 0.099 Angle : 0.525 10.895 14331 Z= 0.263 Chirality : 0.044 0.196 1521 Planarity : 0.003 0.041 1886 Dihedral : 3.790 17.499 1429 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.93 % Allowed : 23.29 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.24), residues: 1325 helix: 1.29 (0.31), residues: 266 sheet: 0.35 (0.36), residues: 242 loop : -0.63 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1190 TYR 0.013 0.001 TYR D1167 PHE 0.009 0.001 PHE C 967 TRP 0.007 0.001 TRP A1155 HIS 0.002 0.000 HIS D 895 Details of bonding type rmsd covalent geometry : bond 0.00230 (10443) covalent geometry : angle 0.52246 (14215) SS BOND : bond 0.00212 ( 58) SS BOND : angle 0.76244 ( 116) hydrogen bonds : bond 0.03064 ( 366) hydrogen bonds : angle 4.66215 ( 984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1617.46 seconds wall clock time: 28 minutes 46.32 seconds (1726.32 seconds total)