Starting phenix.real_space_refine on Sun Aug 24 07:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.map" model { file = "/net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2x_13783/08_2025/7q2x_13783.cif" } resolution = 3.0 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= 0.007 sd= 0.059 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: 8 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11373 2.51 5 N 3057 2.21 5 O 3633 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 18240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3413 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3102 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2279 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7906 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 756 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.32, per 1000 atoms: 0.24 Number of scatterers: 18240 At special positions: 0 Unit cell: (121.98, 147.66, 161.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 91 16.00 P 76 15.00 Mg 2 11.99 F 6 9.00 O 3633 8.00 N 3057 7.00 C 11373 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D1059 " - pdb=" SG CYS D1071 " distance=2.88 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: 1.36 Conformation dependent library (CDL) restraints added in 882.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 67.3% alpha, 8.3% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.929A pdb=" N LEU A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.644A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.503A pdb=" N MET A 156 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.623A pdb=" N ALA A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 228 Proline residue: A 205 - end of helix removed outlier: 3.985A pdb=" N ARG A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 978 removed outlier: 4.074A pdb=" N LYS A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1048 removed outlier: 4.157A pdb=" N MET A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1065 Processing helix chain 'A' and resid 1085 through 1104 Processing helix chain 'A' and resid 1119 through 1132 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.029A pdb=" N PHE A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.925A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 335 through 350 removed outlier: 4.302A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1287 Processing helix chain 'B' and resid 1300 through 1305 removed outlier: 4.084A pdb=" N GLU B1304 " --> pdb=" O ASP B1300 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B1305 " --> pdb=" O PRO B1301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1300 through 1305' Processing helix chain 'B' and resid 1324 through 1343 Processing helix chain 'B' and resid 1358 through 1372 Processing helix chain 'B' and resid 1384 through 1390 removed outlier: 3.717A pdb=" N PHE B1388 " --> pdb=" O ARG B1384 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B1390 " --> pdb=" O ASN B1386 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 71 through 104 Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.543A pdb=" N THR C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 174 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 198 removed outlier: 4.262A pdb=" N GLY C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 300 through 311 removed outlier: 3.816A pdb=" N GLN C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 4.425A pdb=" N ASP C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 669 removed outlier: 3.581A pdb=" N LYS C 669 " --> pdb=" O HIS C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 701 Processing helix chain 'C' and resid 704 through 711 removed outlier: 3.718A pdb=" N ASP C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 727 removed outlier: 3.786A pdb=" N CYS C 716 " --> pdb=" O SER C 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 27 through 41 removed outlier: 4.151A pdb=" N VAL D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 removed outlier: 3.645A pdb=" N ILE D 45 " --> pdb=" O PRO D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 66 through 92 Processing helix chain 'D' and resid 104 through 128 Processing helix chain 'D' and resid 154 through 177 removed outlier: 4.199A pdb=" N ILE D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 204 removed outlier: 3.671A pdb=" N LYS D 189 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 206 through 212 removed outlier: 4.080A pdb=" N THR D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 removed outlier: 3.527A pdb=" N HIS D 230 " --> pdb=" O CYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 288 through 305 Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.597A pdb=" N MET D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 4.006A pdb=" N THR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 322 Processing helix chain 'D' and resid 324 through 342 removed outlier: 3.744A pdb=" N ARG D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 352 through 366 Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.554A pdb=" N ARG D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 407 removed outlier: 4.122A pdb=" N ALA D 397 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 440 through 457 Processing helix chain 'D' and resid 518 through 551 Processing helix chain 'D' and resid 555 through 572 removed outlier: 3.529A pdb=" N VAL D 559 " --> pdb=" O ASN D 555 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.851A pdb=" N HIS D 586 " --> pdb=" O LYS D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 620 through 638 removed outlier: 3.626A pdb=" N GLY D 638 " --> pdb=" O ASN D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 657 Processing helix chain 'D' and resid 662 through 674 Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.851A pdb=" N ALA D 713 " --> pdb=" O MET D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 720 removed outlier: 4.178A pdb=" N ALA D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 731 through 737 removed outlier: 3.757A pdb=" N LYS D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 750 removed outlier: 3.755A pdb=" N CYS D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 781 removed outlier: 4.450A pdb=" N VAL D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 803 removed outlier: 3.575A pdb=" N MET D 791 " --> pdb=" O GLU D 787 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 793 " --> pdb=" O TYR D 789 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN D 794 " --> pdb=" O PRO D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 821 removed outlier: 3.726A pdb=" N LEU D 809 " --> pdb=" O LYS D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 875 removed outlier: 3.554A pdb=" N GLU D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 923 Processing helix chain 'D' and resid 932 through 946 Proline residue: D 938 - end of helix Processing helix chain 'D' and resid 946 through 951 Processing helix chain 'D' and resid 952 through 968 Processing helix chain 'D' and resid 970 through 987 Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 990 through 1007 Processing helix chain 'D' and resid 1008 through 1013 removed outlier: 4.015A pdb=" N VAL D1012 " --> pdb=" O PHE D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1023 removed outlier: 3.599A pdb=" N TYR D1020 " --> pdb=" O THR D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1044 Processing helix chain 'D' and resid 1052 through 1059 removed outlier: 3.522A pdb=" N MET D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1062 No H-bonds generated for 'chain 'D' and resid 1060 through 1062' Processing helix chain 'D' and resid 1064 through 1078 removed outlier: 4.285A pdb=" N MET D1070 " --> pdb=" O GLY D1066 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1082 No H-bonds generated for 'chain 'D' and resid 1080 through 1082' Processing helix chain 'D' and resid 1083 through 1100 removed outlier: 3.577A pdb=" N ASN D1087 " --> pdb=" O ASN D1083 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE D1090 " --> pdb=" O TYR D1086 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP D1091 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1116 removed outlier: 3.853A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1136 removed outlier: 3.814A pdb=" N ARG D1136 " --> pdb=" O VAL D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.508A pdb=" N ILE D1147 " --> pdb=" O GLN D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1148 through 1154 removed outlier: 3.626A pdb=" N ASN D1152 " --> pdb=" O ALA D1148 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1168 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 7.001A pdb=" N THR A 16 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY A 10 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A 3 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP A 84 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 5 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.850A pdb=" N ILE A 145 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR A1109 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A1142 " --> pdb=" O TYR A1109 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A1111 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 29 " --> pdb=" O PHE A1156 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR A1158 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 31 " --> pdb=" O THR A1158 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N PHE A1160 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1051 through 1057 removed outlier: 3.719A pdb=" N ILE A1076 " --> pdb=" O LEU A1073 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 173 removed outlier: 5.327A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 5.327A pdb=" N LEU B 154 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 239 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE B 156 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 237 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 158 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 270 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 299 through 300 removed outlier: 7.572A pdb=" N PHE B 180 " --> pdb=" O GLN B1393 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL B1395 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 182 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B1397 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 184 " --> pdb=" O VAL B1397 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LYS B1399 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id=AA8, first strand: chain 'C' and resid 690 through 691 1052 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3160 1.33 - 1.45: 4673 1.45 - 1.57: 10517 1.57 - 1.69: 148 1.69 - 1.81: 153 Bond restraints: 18651 Sorted by residual: bond pdb=" F2 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" F2 BEF B2002 " pdb="BE BEF B2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" F3 BEF A2002 " pdb="BE BEF A2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F3 BEF B2002 " pdb="BE BEF B2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" F1 BEF B2002 " pdb="BE BEF B2002 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25243 2.49 - 4.99: 159 4.99 - 7.48: 23 7.48 - 9.97: 2 9.97 - 12.47: 2 Bond angle restraints: 25429 Sorted by residual: angle pdb=" F2 BEF A2002 " pdb="BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 119.96 107.49 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" F2 BEF B2002 " pdb="BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 119.96 107.58 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N PRO A 158 " pdb=" CA PRO A 158 " pdb=" CB PRO A 158 " ideal model delta sigma weight residual 103.30 99.74 3.56 1.12e+00 7.97e-01 1.01e+01 angle pdb=" F1 BEF A2002 " pdb="BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" F1 BEF B2002 " pdb="BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.25e+00 ... (remaining 25424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 10878 35.96 - 71.93: 442 71.93 - 107.89: 19 107.89 - 143.85: 1 143.85 - 179.82: 3 Dihedral angle restraints: 11343 sinusoidal: 5196 harmonic: 6147 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 101.82 -161.81 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PA ADP B2001 " pdb=" PB ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 85.28 -145.28 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PB ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 69.77 -129.78 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 11340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2057 0.032 - 0.063: 625 0.063 - 0.095: 195 0.095 - 0.127: 80 0.127 - 0.159: 6 Chirality restraints: 2963 Sorted by residual: chirality pdb=" CA THR D 186 " pdb=" N THR D 186 " pdb=" C THR D 186 " pdb=" CB THR D 186 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE C 731 " pdb=" N ILE C 731 " pdb=" C ILE C 731 " pdb=" CB ILE C 731 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2960 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 305 " 0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO D 306 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 306 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 306 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 312 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B 313 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1345 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO B1346 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1346 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1346 " -0.028 5.00e-02 4.00e+02 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 146 2.61 - 3.18: 15940 3.18 - 3.75: 29200 3.75 - 4.33: 38590 4.33 - 4.90: 62950 Nonbonded interactions: 146826 Sorted by model distance: nonbonded pdb=" F1 BEF B2002 " pdb="MG MG B2003 " model vdw 2.035 2.120 nonbonded pdb=" O2B ADP A2001 " pdb="MG MG A2003 " model vdw 2.063 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B2003 " model vdw 2.085 2.170 nonbonded pdb=" OE1 GLN B 302 " pdb="MG MG B2003 " model vdw 2.133 2.170 nonbonded pdb=" OG SER A 39 " pdb="MG MG A2003 " model vdw 2.143 2.170 ... (remaining 146821 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.007 0.844 18652 Z= 0.335 Angle : 0.598 27.968 25431 Z= 0.308 Chirality : 0.037 0.159 2963 Planarity : 0.004 0.098 2951 Dihedral : 17.519 179.817 7320 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.58 % 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: 2.57 (0.19), residues: 2054 helix: 2.71 (0.15), residues: 1260 sheet: 1.48 (0.39), residues: 180 loop : -0.44 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1384 TYR 0.012 0.001 TYR D 655 PHE 0.022 0.001 PHE B1308 TRP 0.009 0.001 TRP A1033 HIS 0.002 0.000 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00247 (18651) covalent geometry : angle 0.54647 (25429) SS BOND : bond 0.84433 ( 1) SS BOND : angle 27.42818 ( 2) hydrogen bonds : bond 0.11821 ( 1115) hydrogen bonds : angle 4.49272 ( 3222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 0.682 Fit side-chains REVERT: A 107 VAL cc_start: 0.8294 (p) cc_final: 0.8072 (p) REVERT: A 1003 MET cc_start: 0.7791 (mtp) cc_final: 0.7568 (mtm) REVERT: A 1148 MET cc_start: 0.7876 (tpp) cc_final: 0.7640 (tpp) REVERT: B 331 ILE cc_start: 0.7849 (mp) cc_final: 0.7637 (mp) REVERT: B 1327 GLU cc_start: 0.6754 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 1388 PHE cc_start: 0.7183 (p90) cc_final: 0.6825 (p90) REVERT: C 70 ILE cc_start: 0.7947 (pt) cc_final: 0.7714 (mt) REVERT: D 244 LEU cc_start: 0.7011 (tp) cc_final: 0.6658 (tp) REVERT: D 413 LEU cc_start: 0.7255 (tp) cc_final: 0.7005 (tp) REVERT: D 555 ASN cc_start: 0.7259 (t0) cc_final: 0.7007 (t0) REVERT: D 558 GLU cc_start: 0.6871 (tt0) cc_final: 0.6583 (tt0) REVERT: D 748 LEU cc_start: 0.8689 (tp) cc_final: 0.8264 (tp) REVERT: D 964 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6408 (mt-10) REVERT: D 1077 GLU cc_start: 0.6307 (tm-30) cc_final: 0.6023 (tm-30) outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 0.6533 time to fit residues: 320.3191 Evaluate side-chains 389 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 106 GLN B 171 GLN B 266 ASN B 307 ASN B1322 ASN C 307 ASN C 314 GLN C 653 ASN C 665 HIS C 725 ASN C 738 ASN D 70 GLN D 83 ASN D 163 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN D 541 HIS ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 GLN D1062 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123290 restraints weight = 24829.866| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.87 r_work: 0.3328 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 18652 Z= 0.348 Angle : 0.809 11.168 25431 Z= 0.420 Chirality : 0.049 0.230 2963 Planarity : 0.005 0.071 2951 Dihedral : 18.657 175.366 3085 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.42 % Allowed : 12.20 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.18), residues: 2054 helix: 2.02 (0.14), residues: 1272 sheet: 1.07 (0.39), residues: 183 loop : -0.69 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 416 TYR 0.027 0.003 TYR D 529 PHE 0.036 0.003 PHE B 180 TRP 0.013 0.003 TRP C 49 HIS 0.013 0.002 HIS D1024 Details of bonding type rmsd covalent geometry : bond 0.00824 (18651) covalent geometry : angle 0.80940 (25429) SS BOND : bond 0.01431 ( 1) SS BOND : angle 1.05321 ( 2) hydrogen bonds : bond 0.05813 ( 1115) hydrogen bonds : angle 4.00312 ( 3222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 544 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8209 (m-30) cc_final: 0.7975 (m-30) REVERT: A 53 SER cc_start: 0.8303 (t) cc_final: 0.8017 (p) REVERT: A 69 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.7958 (mtp180) REVERT: A 71 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8263 (mp-120) REVERT: A 140 ASN cc_start: 0.8320 (m-40) cc_final: 0.8114 (t0) REVERT: A 159 SER cc_start: 0.8392 (m) cc_final: 0.7985 (p) REVERT: A 173 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (ptm) REVERT: A 177 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.6853 (tpp-160) REVERT: A 182 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 185 MET cc_start: 0.8047 (mtt) cc_final: 0.7818 (mtm) REVERT: A 206 LYS cc_start: 0.7862 (mttm) cc_final: 0.7602 (mptt) REVERT: A 213 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 228 GLU cc_start: 0.7426 (mp0) cc_final: 0.7173 (mp0) REVERT: A 1082 ILE cc_start: 0.8642 (pt) cc_final: 0.8367 (mt) REVERT: A 1083 GLU cc_start: 0.8049 (pt0) cc_final: 0.7764 (pt0) REVERT: A 1104 ARG cc_start: 0.8743 (ttt-90) cc_final: 0.8487 (ttp80) REVERT: A 1113 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 1115 ASP cc_start: 0.8629 (p0) cc_final: 0.8388 (p0) REVERT: A 1131 LYS cc_start: 0.8731 (tttp) cc_final: 0.8501 (tttm) REVERT: A 1140 ILE cc_start: 0.8429 (pt) cc_final: 0.8208 (mt) REVERT: A 1143 SER cc_start: 0.8511 (p) cc_final: 0.8286 (t) REVERT: B 211 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7911 (mm-40) REVERT: B 267 SER cc_start: 0.8081 (m) cc_final: 0.7823 (m) REVERT: B 275 LYS cc_start: 0.8203 (pptt) cc_final: 0.7880 (pttt) REVERT: B 281 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7497 (tp30) REVERT: B 328 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 331 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7803 (mm) REVERT: B 1275 SER cc_start: 0.8472 (m) cc_final: 0.8248 (m) REVERT: B 1318 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7904 (mtp85) REVERT: B 1321 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 1372 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8037 (ttm110) REVERT: B 1399 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8691 (ttpp) REVERT: C 197 GLU cc_start: 0.8252 (tp30) cc_final: 0.7902 (tp30) REVERT: C 213 THR cc_start: 0.8753 (p) cc_final: 0.8430 (p) REVERT: C 277 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6899 (mm-30) REVERT: C 281 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7959 (mt) REVERT: C 642 SER cc_start: 0.8353 (t) cc_final: 0.8056 (p) REVERT: C 713 THR cc_start: 0.8474 (t) cc_final: 0.8048 (m) REVERT: C 739 ASP cc_start: 0.7919 (t0) cc_final: 0.7705 (t0) REVERT: D 119 ILE cc_start: 0.8243 (tp) cc_final: 0.8036 (tp) REVERT: D 202 VAL cc_start: 0.8665 (t) cc_final: 0.8446 (p) REVERT: D 225 MET cc_start: 0.8839 (mtm) cc_final: 0.8616 (mtt) REVERT: D 232 GLN cc_start: 0.7503 (pt0) cc_final: 0.7280 (pt0) REVERT: D 264 GLU cc_start: 0.7634 (mp0) cc_final: 0.7301 (mp0) REVERT: D 269 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7873 (mm-40) REVERT: D 287 ASP cc_start: 0.8341 (p0) cc_final: 0.7844 (p0) REVERT: D 313 MET cc_start: 0.8582 (tpt) cc_final: 0.8255 (tpt) REVERT: D 353 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7719 (mtmm) REVERT: D 365 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7703 (tm-30) REVERT: D 434 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6044 (pp) REVERT: D 548 SER cc_start: 0.8420 (t) cc_final: 0.8095 (m) REVERT: D 558 GLU cc_start: 0.8108 (tt0) cc_final: 0.7697 (tt0) REVERT: D 606 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 643 ASP cc_start: 0.7907 (m-30) cc_final: 0.7707 (m-30) REVERT: D 648 GLU cc_start: 0.8012 (tt0) cc_final: 0.7795 (tt0) REVERT: D 736 LYS cc_start: 0.8335 (mmtp) cc_final: 0.8017 (mmmm) REVERT: D 748 LEU cc_start: 0.8516 (tp) cc_final: 0.8057 (tt) REVERT: D 751 MET cc_start: 0.7218 (ptm) cc_final: 0.6730 (ptt) REVERT: D 768 GLU cc_start: 0.7657 (tt0) cc_final: 0.7318 (tt0) REVERT: D 773 LYS cc_start: 0.8473 (tttm) cc_final: 0.8229 (ttmm) REVERT: D 778 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (pt) REVERT: D 804 SER cc_start: 0.8831 (p) cc_final: 0.8513 (m) REVERT: D 808 ILE cc_start: 0.8091 (mp) cc_final: 0.7792 (mm) REVERT: D 816 GLU cc_start: 0.8045 (tt0) cc_final: 0.7651 (tt0) REVERT: D 839 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8276 (mtt90) REVERT: D 862 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7923 (mm-30) REVERT: D 964 GLU cc_start: 0.8127 (mt-10) cc_final: 0.6940 (tt0) REVERT: D 975 GLU cc_start: 0.7959 (tp30) cc_final: 0.7733 (tp30) REVERT: D 1004 MET cc_start: 0.8357 (mtt) cc_final: 0.8122 (mtp) outliers start: 65 outliers final: 18 residues processed: 570 average time/residue: 0.6671 time to fit residues: 426.1514 Evaluate side-chains 517 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 491 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 770 VAL Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1124 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 132 GLN A1075 ASN B1283 GLN B1385 ASN C 307 ASN C 725 ASN C 738 ASN D 163 GLN D 555 ASN D 610 GLN D 781 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126688 restraints weight = 24990.324| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.74 r_work: 0.3392 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18652 Z= 0.124 Angle : 0.566 9.966 25431 Z= 0.295 Chirality : 0.039 0.173 2963 Planarity : 0.003 0.057 2951 Dihedral : 18.402 176.503 3085 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.26 % Allowed : 18.35 % Favored : 78.39 % 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: 2.23 (0.19), residues: 2054 helix: 2.45 (0.14), residues: 1276 sheet: 1.09 (0.39), residues: 181 loop : -0.60 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1157 TYR 0.020 0.001 TYR D 529 PHE 0.024 0.001 PHE B1388 TRP 0.009 0.001 TRP A1033 HIS 0.003 0.000 HIS D1024 Details of bonding type rmsd covalent geometry : bond 0.00270 (18651) covalent geometry : angle 0.56569 (25429) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.82944 ( 2) hydrogen bonds : bond 0.03989 ( 1115) hydrogen bonds : angle 3.60028 ( 3222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 496 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8196 (m-30) cc_final: 0.7955 (m-30) REVERT: A 53 SER cc_start: 0.8187 (t) cc_final: 0.7959 (p) REVERT: A 69 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7530 (mtp180) REVERT: A 71 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8062 (mp-120) REVERT: A 159 SER cc_start: 0.8352 (m) cc_final: 0.8019 (p) REVERT: A 177 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6663 (tpp-160) REVERT: A 213 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 228 GLU cc_start: 0.7310 (mp0) cc_final: 0.6868 (mp0) REVERT: A 1016 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: A 1104 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8340 (ttp80) REVERT: A 1131 LYS cc_start: 0.8682 (tttp) cc_final: 0.8400 (tttm) REVERT: B 163 ASN cc_start: 0.8556 (m110) cc_final: 0.8273 (m-40) REVERT: B 211 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7870 (mm-40) REVERT: B 275 LYS cc_start: 0.8101 (pptt) cc_final: 0.7804 (pttt) REVERT: B 281 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7424 (tp30) REVERT: B 328 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 1275 SER cc_start: 0.8381 (m) cc_final: 0.8163 (m) REVERT: B 1327 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 1354 ASP cc_start: 0.8451 (p0) cc_final: 0.8246 (p0) REVERT: B 1358 ASP cc_start: 0.7695 (t0) cc_final: 0.7476 (t0) REVERT: B 1372 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7919 (ttm110) REVERT: C 43 ILE cc_start: 0.7985 (mt) cc_final: 0.7754 (mt) REVERT: C 70 ILE cc_start: 0.8158 (pt) cc_final: 0.7856 (mp) REVERT: C 197 GLU cc_start: 0.8223 (tp30) cc_final: 0.7875 (tp30) REVERT: C 213 THR cc_start: 0.8577 (p) cc_final: 0.8276 (p) REVERT: C 277 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 281 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7932 (mt) REVERT: C 303 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6534 (tm-30) REVERT: C 713 THR cc_start: 0.8249 (t) cc_final: 0.7912 (m) REVERT: C 739 ASP cc_start: 0.7599 (t0) cc_final: 0.7345 (t0) REVERT: D 119 ILE cc_start: 0.8165 (tp) cc_final: 0.7916 (tp) REVERT: D 175 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (mt) REVERT: D 195 LEU cc_start: 0.8757 (tt) cc_final: 0.8543 (tp) REVERT: D 202 VAL cc_start: 0.8687 (t) cc_final: 0.8461 (p) REVERT: D 242 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (p) REVERT: D 264 GLU cc_start: 0.7676 (mp0) cc_final: 0.7256 (mp0) REVERT: D 266 ASN cc_start: 0.8060 (p0) cc_final: 0.7733 (p0) REVERT: D 269 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7719 (mm-40) REVERT: D 313 MET cc_start: 0.8557 (tpt) cc_final: 0.8181 (tpt) REVERT: D 365 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 369 ASP cc_start: 0.7565 (t0) cc_final: 0.7082 (t70) REVERT: D 371 ASN cc_start: 0.8364 (t0) cc_final: 0.8007 (t0) REVERT: D 405 ARG cc_start: 0.8730 (ttp-170) cc_final: 0.8367 (ttp-110) REVERT: D 448 LEU cc_start: 0.8010 (tp) cc_final: 0.7763 (tm) REVERT: D 544 ILE cc_start: 0.7528 (mt) cc_final: 0.7221 (tt) REVERT: D 558 GLU cc_start: 0.8072 (tt0) cc_final: 0.7782 (tt0) REVERT: D 606 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6825 (tm-30) REVERT: D 610 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7919 (mp10) REVERT: D 643 ASP cc_start: 0.7825 (m-30) cc_final: 0.7584 (m-30) REVERT: D 658 LYS cc_start: 0.8577 (tppp) cc_final: 0.8202 (mmmm) REVERT: D 714 ASP cc_start: 0.7184 (t0) cc_final: 0.6884 (t0) REVERT: D 736 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8058 (mmmm) REVERT: D 748 LEU cc_start: 0.8344 (tp) cc_final: 0.7978 (tp) REVERT: D 751 MET cc_start: 0.6973 (ptm) cc_final: 0.6476 (ptt) REVERT: D 768 GLU cc_start: 0.7547 (tt0) cc_final: 0.7299 (tt0) REVERT: D 773 LYS cc_start: 0.8340 (tttm) cc_final: 0.8056 (ttmm) REVERT: D 778 ILE cc_start: 0.8253 (tt) cc_final: 0.7954 (pt) REVERT: D 797 SER cc_start: 0.8658 (t) cc_final: 0.8376 (m) REVERT: D 804 SER cc_start: 0.8798 (p) cc_final: 0.8447 (m) REVERT: D 839 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8095 (mtt90) REVERT: D 964 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6981 (mt-10) REVERT: D 975 GLU cc_start: 0.7888 (tp30) cc_final: 0.7682 (tp30) REVERT: D 1032 ARG cc_start: 0.8375 (tpt170) cc_final: 0.8103 (mtp85) outliers start: 62 outliers final: 26 residues processed: 521 average time/residue: 0.7114 time to fit residues: 412.2369 Evaluate side-chains 513 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 482 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 1012 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 63 GLN A 125 GLN A 132 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN B 171 GLN B 288 ASN B1283 GLN C 307 ASN C 660 ASN C 725 ASN D 371 ASN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.150210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119494 restraints weight = 24779.790| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.87 r_work: 0.3311 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18652 Z= 0.245 Angle : 0.660 12.084 25431 Z= 0.341 Chirality : 0.043 0.189 2963 Planarity : 0.004 0.059 2951 Dihedral : 18.570 172.685 3085 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.21 % Allowed : 20.35 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.92 (0.18), residues: 2054 helix: 2.27 (0.14), residues: 1271 sheet: 0.78 (0.39), residues: 185 loop : -0.78 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1157 TYR 0.023 0.002 TYR D 529 PHE 0.026 0.002 PHE D 431 TRP 0.010 0.002 TRP A1033 HIS 0.008 0.001 HIS D1024 Details of bonding type rmsd covalent geometry : bond 0.00581 (18651) covalent geometry : angle 0.66041 (25429) SS BOND : bond 0.00337 ( 1) SS BOND : angle 0.52068 ( 2) hydrogen bonds : bond 0.05033 ( 1115) hydrogen bonds : angle 3.75086 ( 3222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 520 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8261 (t) cc_final: 0.7933 (p) REVERT: A 71 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8130 (mp-120) REVERT: A 159 SER cc_start: 0.8447 (m) cc_final: 0.8151 (p) REVERT: A 189 GLU cc_start: 0.8172 (tp30) cc_final: 0.7783 (tp30) REVERT: A 195 ASN cc_start: 0.8111 (m-40) cc_final: 0.7790 (m110) REVERT: A 213 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 1001 LYS cc_start: 0.8225 (mmtp) cc_final: 0.8022 (mmtp) REVERT: A 1016 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: A 1020 LYS cc_start: 0.8294 (ttmm) cc_final: 0.8047 (mtpt) REVERT: A 1034 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: A 1082 ILE cc_start: 0.8651 (pt) cc_final: 0.8432 (mm) REVERT: A 1104 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.8463 (ttp80) REVERT: B 163 ASN cc_start: 0.8601 (m110) cc_final: 0.8391 (m-40) REVERT: B 201 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8351 (t) REVERT: B 211 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7975 (mm-40) REVERT: B 272 ILE cc_start: 0.8532 (pt) cc_final: 0.8163 (mt) REVERT: B 275 LYS cc_start: 0.8141 (pptt) cc_final: 0.7831 (pttt) REVERT: B 281 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7413 (tp30) REVERT: B 328 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7561 (mt-10) REVERT: B 1275 SER cc_start: 0.8450 (m) cc_final: 0.8216 (m) REVERT: B 1287 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: B 1327 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 1358 ASP cc_start: 0.7583 (t0) cc_final: 0.7338 (t0) REVERT: B 1392 GLN cc_start: 0.8427 (mt0) cc_final: 0.7943 (mt0) REVERT: B 1412 ILE cc_start: 0.8199 (pt) cc_final: 0.7854 (mm) REVERT: C 94 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8829 (t) REVERT: C 196 ASP cc_start: 0.8232 (t0) cc_final: 0.8006 (m-30) REVERT: C 197 GLU cc_start: 0.8245 (tp30) cc_final: 0.7962 (tp30) REVERT: C 277 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6698 (mm-30) REVERT: C 281 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 637 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7715 (m) REVERT: C 642 SER cc_start: 0.8418 (t) cc_final: 0.8195 (p) REVERT: C 713 THR cc_start: 0.8328 (t) cc_final: 0.8048 (m) REVERT: D 75 TYR cc_start: 0.7672 (t80) cc_final: 0.7425 (t80) REVERT: D 78 SER cc_start: 0.8322 (m) cc_final: 0.7804 (p) REVERT: D 202 VAL cc_start: 0.8719 (t) cc_final: 0.8479 (p) REVERT: D 242 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8382 (p) REVERT: D 264 GLU cc_start: 0.7627 (mp0) cc_final: 0.7244 (mp0) REVERT: D 269 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7724 (mm-40) REVERT: D 365 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 369 ASP cc_start: 0.7929 (t0) cc_final: 0.7707 (t70) REVERT: D 447 TYR cc_start: 0.7222 (m-10) cc_final: 0.7012 (m-10) REVERT: D 558 GLU cc_start: 0.8067 (tt0) cc_final: 0.7741 (tt0) REVERT: D 605 ILE cc_start: 0.8618 (mm) cc_final: 0.8344 (mp) REVERT: D 606 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7198 (tm-30) REVERT: D 714 ASP cc_start: 0.7192 (t0) cc_final: 0.6892 (t0) REVERT: D 736 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8146 (mmmm) REVERT: D 748 LEU cc_start: 0.8479 (tp) cc_final: 0.8030 (tt) REVERT: D 751 MET cc_start: 0.7154 (ptm) cc_final: 0.6811 (ptt) REVERT: D 773 LYS cc_start: 0.8347 (tttm) cc_final: 0.8043 (ttmm) REVERT: D 964 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7471 (mt-10) REVERT: D 975 GLU cc_start: 0.7823 (tp30) cc_final: 0.7602 (tp30) REVERT: D 1014 GLU cc_start: 0.8188 (mp0) cc_final: 0.7642 (mp0) REVERT: D 1025 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: D 1032 ARG cc_start: 0.8426 (tpt170) cc_final: 0.8153 (mtp85) REVERT: D 1049 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (p) outliers start: 80 outliers final: 29 residues processed: 549 average time/residue: 0.6961 time to fit residues: 425.2156 Evaluate side-chains 536 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 497 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 177 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 132 GLN A 142 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 ASN B 288 ASN B1393 GLN C 307 ASN C 660 ASN C 738 ASN D 178 ASN D 322 ASN D 541 HIS D 610 GLN D 781 ASN D 852 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120215 restraints weight = 24642.416| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.86 r_work: 0.3327 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18652 Z= 0.179 Angle : 0.604 10.640 25431 Z= 0.313 Chirality : 0.041 0.199 2963 Planarity : 0.004 0.058 2951 Dihedral : 18.491 172.975 3085 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.42 % Allowed : 21.61 % Favored : 73.97 % 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: 1.98 (0.18), residues: 2054 helix: 2.32 (0.14), residues: 1272 sheet: 0.77 (0.39), residues: 183 loop : -0.77 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1157 TYR 0.019 0.002 TYR D 529 PHE 0.019 0.002 PHE B1388 TRP 0.009 0.001 TRP D 589 HIS 0.005 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00418 (18651) covalent geometry : angle 0.60375 (25429) SS BOND : bond 0.00346 ( 1) SS BOND : angle 0.51237 ( 2) hydrogen bonds : bond 0.04486 ( 1115) hydrogen bonds : angle 3.67141 ( 3222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 480 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8257 (t) cc_final: 0.7910 (p) REVERT: A 69 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7506 (mtp180) REVERT: A 71 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8076 (mp-120) REVERT: A 76 LYS cc_start: 0.8313 (tttp) cc_final: 0.8091 (tttp) REVERT: A 159 SER cc_start: 0.8464 (m) cc_final: 0.8169 (p) REVERT: A 189 GLU cc_start: 0.8121 (tp30) cc_final: 0.7763 (tp30) REVERT: A 195 ASN cc_start: 0.8137 (m-40) cc_final: 0.7825 (m110) REVERT: A 213 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 1012 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7589 (ttm) REVERT: A 1016 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: A 1034 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 1104 ARG cc_start: 0.8750 (ttt-90) cc_final: 0.8448 (ttp80) REVERT: A 1131 LYS cc_start: 0.8690 (tttp) cc_final: 0.8411 (tttm) REVERT: A 1146 GLU cc_start: 0.7857 (tp30) cc_final: 0.7543 (tp30) REVERT: B 201 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8378 (t) REVERT: B 272 ILE cc_start: 0.8522 (pt) cc_final: 0.8209 (mt) REVERT: B 275 LYS cc_start: 0.8175 (pptt) cc_final: 0.7861 (pttt) REVERT: B 281 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7358 (tp30) REVERT: B 331 ILE cc_start: 0.8170 (mm) cc_final: 0.7829 (mm) REVERT: B 1275 SER cc_start: 0.8401 (m) cc_final: 0.8170 (m) REVERT: B 1297 ASP cc_start: 0.7374 (t0) cc_final: 0.6848 (t0) REVERT: B 1327 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 1358 ASP cc_start: 0.7659 (t0) cc_final: 0.7442 (t0) REVERT: C 94 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8821 (t) REVERT: C 196 ASP cc_start: 0.8194 (t0) cc_final: 0.7962 (m-30) REVERT: C 197 GLU cc_start: 0.8234 (tp30) cc_final: 0.7964 (tp30) REVERT: C 277 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6687 (mm-30) REVERT: C 281 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7808 (mt) REVERT: C 637 THR cc_start: 0.8191 (p) cc_final: 0.7932 (m) REVERT: C 642 SER cc_start: 0.8381 (t) cc_final: 0.8156 (p) REVERT: C 713 THR cc_start: 0.8306 (t) cc_final: 0.8087 (m) REVERT: C 729 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 740 LEU cc_start: 0.8740 (mt) cc_final: 0.8489 (mp) REVERT: D 75 TYR cc_start: 0.7694 (t80) cc_final: 0.7445 (t80) REVERT: D 78 SER cc_start: 0.8228 (m) cc_final: 0.7866 (p) REVERT: D 202 VAL cc_start: 0.8704 (t) cc_final: 0.8493 (p) REVERT: D 242 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8360 (p) REVERT: D 264 GLU cc_start: 0.7549 (mp0) cc_final: 0.7228 (mp0) REVERT: D 269 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7700 (mm-40) REVERT: D 272 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7681 (mt-10) REVERT: D 365 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 369 ASP cc_start: 0.7928 (t0) cc_final: 0.7648 (t70) REVERT: D 371 ASN cc_start: 0.8400 (t0) cc_final: 0.8098 (t0) REVERT: D 386 CYS cc_start: 0.7962 (p) cc_final: 0.7682 (m) REVERT: D 427 LEU cc_start: 0.8618 (tp) cc_final: 0.8341 (tt) REVERT: D 448 LEU cc_start: 0.8060 (tp) cc_final: 0.7810 (tm) REVERT: D 522 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6627 (tppp) REVERT: D 605 ILE cc_start: 0.8627 (mm) cc_final: 0.8341 (mp) REVERT: D 606 GLU cc_start: 0.7472 (tm-30) cc_final: 0.6987 (tm-30) REVERT: D 610 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7996 (mp10) REVERT: D 736 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8156 (mmmm) REVERT: D 748 LEU cc_start: 0.8384 (tp) cc_final: 0.8027 (tp) REVERT: D 749 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7414 (tt0) REVERT: D 751 MET cc_start: 0.7069 (ptm) cc_final: 0.6724 (ptt) REVERT: D 773 LYS cc_start: 0.8368 (tttm) cc_final: 0.8100 (ttmm) REVERT: D 776 TYR cc_start: 0.8527 (t80) cc_final: 0.8325 (t80) REVERT: D 783 THR cc_start: 0.8765 (t) cc_final: 0.8559 (p) REVERT: D 867 GLU cc_start: 0.7371 (tt0) cc_final: 0.7071 (tp30) REVERT: D 975 GLU cc_start: 0.7849 (tp30) cc_final: 0.7609 (tp30) REVERT: D 1014 GLU cc_start: 0.8216 (mp0) cc_final: 0.7823 (mp0) REVERT: D 1025 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: D 1049 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7843 (p) REVERT: D 1115 LEU cc_start: 0.8234 (mt) cc_final: 0.7981 (mt) outliers start: 84 outliers final: 38 residues processed: 514 average time/residue: 0.6873 time to fit residues: 394.5849 Evaluate side-chains 515 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 466 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1370 LYS Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN ** B1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1393 GLN C 307 ASN D 322 ASN D 663 HIS D 781 ASN D 852 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119620 restraints weight = 24541.666| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.74 r_work: 0.3298 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18652 Z= 0.243 Angle : 0.657 11.814 25431 Z= 0.340 Chirality : 0.044 0.225 2963 Planarity : 0.004 0.059 2951 Dihedral : 18.566 173.035 3085 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.47 % Allowed : 21.77 % Favored : 72.77 % 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: 1.75 (0.18), residues: 2054 helix: 2.17 (0.14), residues: 1274 sheet: 0.49 (0.38), residues: 185 loop : -0.87 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1157 TYR 0.022 0.002 TYR D 529 PHE 0.021 0.002 PHE D1149 TRP 0.009 0.001 TRP D 589 HIS 0.008 0.001 HIS D 701 Details of bonding type rmsd covalent geometry : bond 0.00574 (18651) covalent geometry : angle 0.65670 (25429) SS BOND : bond 0.00522 ( 1) SS BOND : angle 0.43188 ( 2) hydrogen bonds : bond 0.05010 ( 1115) hydrogen bonds : angle 3.78799 ( 3222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 490 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8293 (t) cc_final: 0.8022 (p) REVERT: A 69 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7344 (mtp180) REVERT: A 71 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8109 (mp-120) REVERT: A 76 LYS cc_start: 0.8345 (tttp) cc_final: 0.8110 (tttp) REVERT: A 159 SER cc_start: 0.8420 (m) cc_final: 0.8133 (p) REVERT: A 187 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8306 (ttmm) REVERT: A 189 GLU cc_start: 0.8142 (tp30) cc_final: 0.7777 (tp30) REVERT: A 213 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 228 GLU cc_start: 0.7614 (mp0) cc_final: 0.7264 (mp0) REVERT: A 1016 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: A 1034 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 1104 ARG cc_start: 0.8793 (ttt-90) cc_final: 0.8481 (ttp80) REVERT: A 1137 SER cc_start: 0.8297 (t) cc_final: 0.7989 (t) REVERT: A 1146 GLU cc_start: 0.7855 (tp30) cc_final: 0.7534 (tp30) REVERT: B 275 LYS cc_start: 0.8262 (pptt) cc_final: 0.7969 (pttt) REVERT: B 331 ILE cc_start: 0.8199 (mm) cc_final: 0.7786 (mm) REVERT: B 1275 SER cc_start: 0.8394 (m) cc_final: 0.8161 (m) REVERT: B 1286 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8165 (p) REVERT: B 1287 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: B 1297 ASP cc_start: 0.7432 (t0) cc_final: 0.6976 (t0) REVERT: B 1358 ASP cc_start: 0.7661 (t0) cc_final: 0.7411 (t0) REVERT: B 1368 TYR cc_start: 0.8619 (t80) cc_final: 0.8368 (t80) REVERT: B 1375 ASN cc_start: 0.8123 (p0) cc_final: 0.7666 (p0) REVERT: C 94 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 196 ASP cc_start: 0.8180 (t0) cc_final: 0.7960 (m-30) REVERT: C 197 GLU cc_start: 0.8207 (tp30) cc_final: 0.7982 (tp30) REVERT: C 277 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6730 (mm-30) REVERT: C 281 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7771 (mt) REVERT: C 637 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7852 (m) REVERT: C 713 THR cc_start: 0.8356 (t) cc_final: 0.8051 (m) REVERT: D 221 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8471 (tpp-160) REVERT: D 242 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8374 (p) REVERT: D 264 GLU cc_start: 0.7533 (mp0) cc_final: 0.7251 (mp0) REVERT: D 269 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7682 (mm-40) REVERT: D 272 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7642 (mt-10) REVERT: D 365 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 369 ASP cc_start: 0.8044 (t0) cc_final: 0.7821 (t70) REVERT: D 370 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (m) REVERT: D 386 CYS cc_start: 0.7928 (p) cc_final: 0.7710 (m) REVERT: D 398 LYS cc_start: 0.8160 (tppp) cc_final: 0.7768 (mmmm) REVERT: D 427 LEU cc_start: 0.8633 (tp) cc_final: 0.8392 (tt) REVERT: D 432 LYS cc_start: 0.8142 (mttt) cc_final: 0.7841 (mttm) REVERT: D 447 TYR cc_start: 0.7376 (m-10) cc_final: 0.7165 (m-10) REVERT: D 448 LEU cc_start: 0.8037 (tp) cc_final: 0.7670 (tm) REVERT: D 452 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 522 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6634 (tppp) REVERT: D 605 ILE cc_start: 0.8615 (mm) cc_final: 0.8355 (mp) REVERT: D 606 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 610 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7875 (mp10) REVERT: D 658 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8287 (mmmm) REVERT: D 714 ASP cc_start: 0.7162 (t0) cc_final: 0.6932 (t0) REVERT: D 736 LYS cc_start: 0.8435 (mmtp) cc_final: 0.8193 (mmmm) REVERT: D 748 LEU cc_start: 0.8385 (tp) cc_final: 0.8044 (tp) REVERT: D 749 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7455 (tt0) REVERT: D 751 MET cc_start: 0.7196 (ptm) cc_final: 0.6909 (ptt) REVERT: D 773 LYS cc_start: 0.8319 (tttm) cc_final: 0.8052 (ttmm) REVERT: D 816 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7889 (tt0) REVERT: D 867 GLU cc_start: 0.7324 (tt0) cc_final: 0.7001 (tp30) REVERT: D 975 GLU cc_start: 0.7814 (tp30) cc_final: 0.7576 (tp30) REVERT: D 1001 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (mt) REVERT: D 1014 GLU cc_start: 0.8293 (mp0) cc_final: 0.7887 (mp0) REVERT: D 1025 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: D 1049 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7891 (p) outliers start: 104 outliers final: 53 residues processed: 537 average time/residue: 0.6898 time to fit residues: 413.0045 Evaluate side-chains 542 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 475 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1108 MET Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 658 LYS Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 35 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 195 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN B1385 ASN B1393 GLN C 307 ASN D 229 ASN D 322 ASN D 371 ASN D 852 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120562 restraints weight = 24848.734| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.81 r_work: 0.3308 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18652 Z= 0.169 Angle : 0.621 12.656 25431 Z= 0.320 Chirality : 0.041 0.229 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.509 171.843 3085 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.52 % Allowed : 23.34 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.18), residues: 2054 helix: 2.31 (0.14), residues: 1270 sheet: 0.53 (0.39), residues: 183 loop : -0.86 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1157 TYR 0.023 0.002 TYR B 326 PHE 0.024 0.002 PHE D 392 TRP 0.009 0.001 TRP D 589 HIS 0.005 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00392 (18651) covalent geometry : angle 0.62113 (25429) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.34592 ( 2) hydrogen bonds : bond 0.04482 ( 1115) hydrogen bonds : angle 3.68568 ( 3222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 483 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8198 (t) cc_final: 0.7867 (p) REVERT: A 69 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7835 (mtp180) REVERT: A 76 LYS cc_start: 0.8319 (tttp) cc_final: 0.8102 (tttp) REVERT: A 159 SER cc_start: 0.8481 (m) cc_final: 0.8199 (p) REVERT: A 189 GLU cc_start: 0.8187 (tp30) cc_final: 0.7835 (tp30) REVERT: A 213 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 1003 MET cc_start: 0.8370 (mtm) cc_final: 0.8160 (mtp) REVERT: A 1016 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: A 1034 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 1104 ARG cc_start: 0.8768 (ttt-90) cc_final: 0.8485 (ttp80) REVERT: A 1131 LYS cc_start: 0.8682 (tttp) cc_final: 0.8399 (tttm) REVERT: A 1137 SER cc_start: 0.8312 (t) cc_final: 0.8053 (t) REVERT: A 1146 GLU cc_start: 0.7852 (tp30) cc_final: 0.7537 (tp30) REVERT: B 275 LYS cc_start: 0.8300 (pptt) cc_final: 0.7991 (pttt) REVERT: B 331 ILE cc_start: 0.8135 (mm) cc_final: 0.7757 (mm) REVERT: B 1286 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 1287 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8002 (mtm) REVERT: B 1297 ASP cc_start: 0.7459 (t0) cc_final: 0.7035 (t0) REVERT: B 1327 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 1358 ASP cc_start: 0.7681 (t0) cc_final: 0.7466 (t0) REVERT: B 1368 TYR cc_start: 0.8617 (t80) cc_final: 0.8308 (t80) REVERT: B 1372 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7969 (ttm110) REVERT: B 1375 ASN cc_start: 0.8149 (p0) cc_final: 0.7685 (p0) REVERT: C 196 ASP cc_start: 0.8158 (t0) cc_final: 0.7918 (m-30) REVERT: C 197 GLU cc_start: 0.8236 (tp30) cc_final: 0.8011 (tp30) REVERT: C 277 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6688 (mm-30) REVERT: C 281 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7849 (mt) REVERT: C 286 ASP cc_start: 0.7564 (t0) cc_final: 0.7314 (t0) REVERT: C 637 THR cc_start: 0.8112 (p) cc_final: 0.7876 (m) REVERT: C 713 THR cc_start: 0.8336 (t) cc_final: 0.8052 (m) REVERT: C 738 ASN cc_start: 0.8658 (t0) cc_final: 0.8406 (t0) REVERT: D 75 TYR cc_start: 0.7973 (t80) cc_final: 0.7729 (t80) REVERT: D 221 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8309 (mmm-85) REVERT: D 242 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (p) REVERT: D 264 GLU cc_start: 0.7576 (mp0) cc_final: 0.7310 (mp0) REVERT: D 269 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7696 (mm-40) REVERT: D 272 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7679 (mt-10) REVERT: D 313 MET cc_start: 0.8520 (tpt) cc_final: 0.8173 (tpt) REVERT: D 365 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 369 ASP cc_start: 0.8023 (t0) cc_final: 0.7816 (t70) REVERT: D 398 LYS cc_start: 0.8060 (tppp) cc_final: 0.7698 (mmmm) REVERT: D 427 LEU cc_start: 0.8645 (tp) cc_final: 0.8401 (tt) REVERT: D 448 LEU cc_start: 0.8036 (tp) cc_final: 0.7721 (tm) REVERT: D 452 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7058 (mm-30) REVERT: D 522 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6688 (tppp) REVERT: D 605 ILE cc_start: 0.8645 (mm) cc_final: 0.8364 (mp) REVERT: D 606 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7032 (tm-30) REVERT: D 610 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7952 (mp10) REVERT: D 748 LEU cc_start: 0.8363 (tp) cc_final: 0.8100 (tp) REVERT: D 749 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7388 (tt0) REVERT: D 773 LYS cc_start: 0.8406 (tttm) cc_final: 0.8152 (ttmm) REVERT: D 816 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7951 (tt0) REVERT: D 867 GLU cc_start: 0.7447 (tt0) cc_final: 0.7134 (tp30) REVERT: D 941 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: D 975 GLU cc_start: 0.7887 (tp30) cc_final: 0.7661 (tp30) REVERT: D 1004 MET cc_start: 0.8109 (mtt) cc_final: 0.7866 (mtp) REVERT: D 1014 GLU cc_start: 0.8297 (mp0) cc_final: 0.7894 (mp0) REVERT: D 1025 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: D 1049 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (p) outliers start: 86 outliers final: 48 residues processed: 522 average time/residue: 0.7042 time to fit residues: 410.3373 Evaluate side-chains 536 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 479 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 941 GLU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 29 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 100 optimal weight: 0.0870 chunk 155 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A1075 ASN B1385 ASN B1393 GLN C 307 ASN C 653 ASN D 322 ASN D 852 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122830 restraints weight = 24766.122| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.84 r_work: 0.3362 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18652 Z= 0.125 Angle : 0.603 11.252 25431 Z= 0.311 Chirality : 0.039 0.191 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.473 172.306 3085 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.68 % Allowed : 24.92 % Favored : 71.40 % 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: 2.06 (0.19), residues: 2054 helix: 2.45 (0.14), residues: 1272 sheet: 0.75 (0.40), residues: 177 loop : -0.87 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1157 TYR 0.025 0.002 TYR D 117 PHE 0.019 0.001 PHE D 392 TRP 0.008 0.001 TRP D 589 HIS 0.004 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00272 (18651) covalent geometry : angle 0.60290 (25429) SS BOND : bond 0.00264 ( 1) SS BOND : angle 0.24453 ( 2) hydrogen bonds : bond 0.03989 ( 1115) hydrogen bonds : angle 3.60989 ( 3222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 466 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8204 (t) cc_final: 0.7826 (p) REVERT: A 69 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7723 (mtp180) REVERT: A 106 GLN cc_start: 0.8310 (mt0) cc_final: 0.8106 (mt0) REVERT: A 159 SER cc_start: 0.8492 (m) cc_final: 0.8198 (p) REVERT: A 185 MET cc_start: 0.8127 (mtp) cc_final: 0.7834 (mtm) REVERT: A 194 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 213 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 228 GLU cc_start: 0.7743 (mp0) cc_final: 0.7385 (mp0) REVERT: A 1016 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: A 1029 LEU cc_start: 0.8341 (tt) cc_final: 0.8138 (tm) REVERT: A 1034 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 1104 ARG cc_start: 0.8692 (ttt-90) cc_final: 0.8419 (ttp80) REVERT: A 1131 LYS cc_start: 0.8644 (tttp) cc_final: 0.8373 (tttm) REVERT: A 1137 SER cc_start: 0.8273 (t) cc_final: 0.8028 (t) REVERT: A 1146 GLU cc_start: 0.7813 (tp30) cc_final: 0.7471 (tp30) REVERT: A 1157 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7662 (ttm-80) REVERT: B 275 LYS cc_start: 0.8174 (pptt) cc_final: 0.7832 (pttt) REVERT: B 281 GLU cc_start: 0.7804 (tp30) cc_final: 0.7432 (tp30) REVERT: B 331 ILE cc_start: 0.8009 (mm) cc_final: 0.7629 (mm) REVERT: B 1286 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 1287 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8035 (mtm) REVERT: B 1297 ASP cc_start: 0.7394 (t0) cc_final: 0.6965 (t0) REVERT: B 1327 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 1358 ASP cc_start: 0.7605 (t0) cc_final: 0.7387 (t0) REVERT: B 1368 TYR cc_start: 0.8597 (t80) cc_final: 0.8315 (t80) REVERT: B 1375 ASN cc_start: 0.8136 (p0) cc_final: 0.7776 (p0) REVERT: B 1392 GLN cc_start: 0.8584 (mt0) cc_final: 0.8238 (mt0) REVERT: C 196 ASP cc_start: 0.8121 (t0) cc_final: 0.7874 (m-30) REVERT: C 197 GLU cc_start: 0.8209 (tp30) cc_final: 0.7938 (tp30) REVERT: C 277 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6398 (mm-30) REVERT: C 281 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7845 (mm) REVERT: C 286 ASP cc_start: 0.7576 (t0) cc_final: 0.7309 (t0) REVERT: C 303 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: C 637 THR cc_start: 0.8160 (p) cc_final: 0.7679 (t) REVERT: C 713 THR cc_start: 0.8306 (t) cc_final: 0.8029 (m) REVERT: D 75 TYR cc_start: 0.7854 (t80) cc_final: 0.7596 (t80) REVERT: D 113 GLU cc_start: 0.7847 (tp30) cc_final: 0.7551 (mt-10) REVERT: D 165 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 166 ASN cc_start: 0.8271 (m-40) cc_final: 0.7926 (t0) REVERT: D 176 GLU cc_start: 0.8006 (tp30) cc_final: 0.7499 (tp30) REVERT: D 195 LEU cc_start: 0.8718 (tt) cc_final: 0.8495 (tp) REVERT: D 202 VAL cc_start: 0.8710 (t) cc_final: 0.8458 (p) REVERT: D 264 GLU cc_start: 0.7571 (mp0) cc_final: 0.7245 (mp0) REVERT: D 266 ASN cc_start: 0.8114 (p0) cc_final: 0.7821 (p0) REVERT: D 269 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7651 (mm-40) REVERT: D 272 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7584 (mt-10) REVERT: D 365 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 369 ASP cc_start: 0.7834 (t0) cc_final: 0.7587 (t70) REVERT: D 371 ASN cc_start: 0.8225 (t0) cc_final: 0.7945 (t0) REVERT: D 427 LEU cc_start: 0.8637 (tp) cc_final: 0.8358 (tt) REVERT: D 448 LEU cc_start: 0.8035 (tp) cc_final: 0.7784 (tm) REVERT: D 452 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7003 (mm-30) REVERT: D 522 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6536 (tppp) REVERT: D 544 ILE cc_start: 0.7692 (mt) cc_final: 0.7287 (tt) REVERT: D 605 ILE cc_start: 0.8640 (mm) cc_final: 0.8396 (mp) REVERT: D 606 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 610 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7878 (mp10) REVERT: D 648 GLU cc_start: 0.7815 (tt0) cc_final: 0.7577 (tt0) REVERT: D 749 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7323 (tt0) REVERT: D 773 LYS cc_start: 0.8418 (tttm) cc_final: 0.8171 (ttmm) REVERT: D 816 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7940 (tt0) REVERT: D 867 GLU cc_start: 0.7431 (tt0) cc_final: 0.7150 (tp30) REVERT: D 935 LYS cc_start: 0.7911 (mttp) cc_final: 0.7608 (mttt) REVERT: D 975 GLU cc_start: 0.7878 (tp30) cc_final: 0.7672 (tp30) REVERT: D 1001 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (mt) REVERT: D 1004 MET cc_start: 0.7982 (mtt) cc_final: 0.7757 (mtp) REVERT: D 1014 GLU cc_start: 0.8268 (mp0) cc_final: 0.7852 (mp0) REVERT: D 1049 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7658 (p) outliers start: 70 outliers final: 39 residues processed: 498 average time/residue: 0.7154 time to fit residues: 396.3996 Evaluate side-chains 509 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 462 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A1075 ASN B1385 ASN B1393 GLN C 307 ASN D 178 ASN D 322 ASN D 429 HIS D 852 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.122241 restraints weight = 24754.257| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.84 r_work: 0.3356 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18652 Z= 0.138 Angle : 0.607 12.961 25431 Z= 0.312 Chirality : 0.040 0.210 2963 Planarity : 0.004 0.059 2951 Dihedral : 18.475 172.172 3085 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.63 % Allowed : 25.71 % Favored : 70.66 % 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: 2.09 (0.19), residues: 2054 helix: 2.46 (0.14), residues: 1271 sheet: 0.74 (0.39), residues: 177 loop : -0.81 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 178 TYR 0.026 0.002 TYR D 117 PHE 0.026 0.001 PHE A1103 TRP 0.008 0.001 TRP D 589 HIS 0.003 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00312 (18651) covalent geometry : angle 0.60672 (25429) SS BOND : bond 0.00301 ( 1) SS BOND : angle 0.20877 ( 2) hydrogen bonds : bond 0.04109 ( 1115) hydrogen bonds : angle 3.64140 ( 3222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 472 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8193 (t) cc_final: 0.7812 (p) REVERT: A 76 LYS cc_start: 0.8239 (tttp) cc_final: 0.7715 (tttp) REVERT: A 159 SER cc_start: 0.8462 (m) cc_final: 0.8165 (p) REVERT: A 177 ARG cc_start: 0.7352 (tpp-160) cc_final: 0.6889 (tpm-80) REVERT: A 213 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 1016 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: A 1034 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 1104 ARG cc_start: 0.8746 (ttt-90) cc_final: 0.8464 (ttp80) REVERT: A 1131 LYS cc_start: 0.8634 (tttp) cc_final: 0.8353 (tttm) REVERT: A 1137 SER cc_start: 0.8230 (t) cc_final: 0.7972 (t) REVERT: A 1146 GLU cc_start: 0.7823 (tp30) cc_final: 0.7492 (tp30) REVERT: A 1157 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7650 (ttm-80) REVERT: B 275 LYS cc_start: 0.8172 (pptt) cc_final: 0.7842 (pttt) REVERT: B 281 GLU cc_start: 0.7830 (tp30) cc_final: 0.7472 (tp30) REVERT: B 331 ILE cc_start: 0.7976 (mm) cc_final: 0.7581 (mm) REVERT: B 1268 MET cc_start: 0.8061 (mmm) cc_final: 0.7839 (tpp) REVERT: B 1286 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8039 (p) REVERT: B 1287 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8038 (mtm) REVERT: B 1294 GLU cc_start: 0.7668 (pt0) cc_final: 0.7452 (pt0) REVERT: B 1297 ASP cc_start: 0.7398 (t0) cc_final: 0.6965 (t0) REVERT: B 1309 SER cc_start: 0.8711 (p) cc_final: 0.8416 (p) REVERT: B 1310 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8449 (p) REVERT: B 1327 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 1358 ASP cc_start: 0.7628 (t0) cc_final: 0.7408 (t0) REVERT: B 1368 TYR cc_start: 0.8604 (t80) cc_final: 0.8366 (t80) REVERT: B 1375 ASN cc_start: 0.8123 (p0) cc_final: 0.7666 (p0) REVERT: B 1385 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6963 (m110) REVERT: B 1392 GLN cc_start: 0.8560 (mt0) cc_final: 0.8245 (mt0) REVERT: C 196 ASP cc_start: 0.8134 (t0) cc_final: 0.7881 (m-30) REVERT: C 197 GLU cc_start: 0.8218 (tp30) cc_final: 0.7971 (tp30) REVERT: C 277 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6486 (mm-30) REVERT: C 281 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (mt) REVERT: C 286 ASP cc_start: 0.7554 (t0) cc_final: 0.7294 (t0) REVERT: C 303 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6933 (mm-30) REVERT: C 637 THR cc_start: 0.8198 (p) cc_final: 0.7746 (t) REVERT: C 713 THR cc_start: 0.8342 (t) cc_final: 0.8100 (m) REVERT: C 738 ASN cc_start: 0.8708 (t0) cc_final: 0.8350 (t0) REVERT: D 75 TYR cc_start: 0.7887 (t80) cc_final: 0.7633 (t80) REVERT: D 113 GLU cc_start: 0.7858 (tp30) cc_final: 0.7605 (mt-10) REVERT: D 165 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 166 ASN cc_start: 0.8293 (m-40) cc_final: 0.7952 (t0) REVERT: D 176 GLU cc_start: 0.8000 (tp30) cc_final: 0.7531 (tp30) REVERT: D 195 LEU cc_start: 0.8714 (tt) cc_final: 0.8461 (tp) REVERT: D 202 VAL cc_start: 0.8706 (t) cc_final: 0.8462 (p) REVERT: D 221 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8417 (tpp-160) REVERT: D 264 GLU cc_start: 0.7565 (mp0) cc_final: 0.7266 (mp0) REVERT: D 272 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7595 (mt-10) REVERT: D 365 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 427 LEU cc_start: 0.8633 (tp) cc_final: 0.8371 (tt) REVERT: D 448 LEU cc_start: 0.8044 (tp) cc_final: 0.7785 (tm) REVERT: D 452 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7010 (mm-30) REVERT: D 522 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6562 (tppp) REVERT: D 561 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: D 605 ILE cc_start: 0.8609 (mm) cc_final: 0.8353 (mp) REVERT: D 606 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 610 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7919 (mp10) REVERT: D 648 GLU cc_start: 0.7812 (tt0) cc_final: 0.7562 (tt0) REVERT: D 749 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7355 (tt0) REVERT: D 773 LYS cc_start: 0.8434 (tttm) cc_final: 0.8188 (ttmm) REVERT: D 816 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7966 (tt0) REVERT: D 867 GLU cc_start: 0.7472 (tt0) cc_final: 0.7166 (tp30) REVERT: D 926 LEU cc_start: 0.8495 (pp) cc_final: 0.8283 (pt) REVERT: D 935 LYS cc_start: 0.7952 (mttp) cc_final: 0.7637 (mttt) REVERT: D 975 GLU cc_start: 0.7867 (tp30) cc_final: 0.7518 (tp30) REVERT: D 1001 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 1004 MET cc_start: 0.8037 (mtt) cc_final: 0.7783 (mtp) REVERT: D 1011 LEU cc_start: 0.8186 (mp) cc_final: 0.7886 (mt) REVERT: D 1014 GLU cc_start: 0.8280 (mp0) cc_final: 0.7863 (mp0) REVERT: D 1025 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: D 1049 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7666 (p) outliers start: 69 outliers final: 40 residues processed: 504 average time/residue: 0.7127 time to fit residues: 398.8881 Evaluate side-chains 516 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 464 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1385 ASN Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1075 ASN B1385 ASN B1393 GLN C 307 ASN D 178 ASN D 229 ASN D 634 ASN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122961 restraints weight = 24661.103| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.84 r_work: 0.3367 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18652 Z= 0.131 Angle : 0.626 17.730 25431 Z= 0.317 Chirality : 0.040 0.212 2963 Planarity : 0.004 0.063 2951 Dihedral : 18.447 171.698 3085 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.47 % Allowed : 26.50 % Favored : 70.03 % 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: 2.11 (0.19), residues: 2054 helix: 2.48 (0.14), residues: 1272 sheet: 0.66 (0.39), residues: 179 loop : -0.78 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 178 TYR 0.027 0.002 TYR D 117 PHE 0.025 0.001 PHE A1103 TRP 0.008 0.001 TRP D 589 HIS 0.003 0.001 HIS D 541 Details of bonding type rmsd covalent geometry : bond 0.00292 (18651) covalent geometry : angle 0.62563 (25429) SS BOND : bond 0.00278 ( 1) SS BOND : angle 0.16537 ( 2) hydrogen bonds : bond 0.04027 ( 1115) hydrogen bonds : angle 3.64799 ( 3222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 463 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8168 (t) cc_final: 0.7812 (p) REVERT: A 159 SER cc_start: 0.8496 (m) cc_final: 0.8201 (p) REVERT: A 177 ARG cc_start: 0.7338 (tpp-160) cc_final: 0.6865 (tpm-80) REVERT: A 213 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 228 GLU cc_start: 0.7497 (mp0) cc_final: 0.7263 (mp0) REVERT: A 1016 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: A 1034 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 1104 ARG cc_start: 0.8674 (ttt-90) cc_final: 0.8416 (ttp80) REVERT: A 1131 LYS cc_start: 0.8626 (tttp) cc_final: 0.8363 (tttm) REVERT: A 1137 SER cc_start: 0.8247 (t) cc_final: 0.7983 (t) REVERT: A 1146 GLU cc_start: 0.7821 (tp30) cc_final: 0.7494 (tp30) REVERT: A 1157 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7413 (ttm-80) REVERT: B 275 LYS cc_start: 0.8151 (pptt) cc_final: 0.7828 (pttt) REVERT: B 281 GLU cc_start: 0.7802 (tp30) cc_final: 0.7446 (tp30) REVERT: B 331 ILE cc_start: 0.7940 (mm) cc_final: 0.7538 (mm) REVERT: B 1268 MET cc_start: 0.8057 (mmm) cc_final: 0.7827 (tpp) REVERT: B 1286 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8007 (p) REVERT: B 1287 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8062 (mtm) REVERT: B 1294 GLU cc_start: 0.7651 (pt0) cc_final: 0.7436 (pt0) REVERT: B 1297 ASP cc_start: 0.7368 (t0) cc_final: 0.6939 (t0) REVERT: B 1309 SER cc_start: 0.8708 (p) cc_final: 0.8377 (p) REVERT: B 1310 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 1327 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 1358 ASP cc_start: 0.7625 (t0) cc_final: 0.7401 (t0) REVERT: B 1368 TYR cc_start: 0.8591 (t80) cc_final: 0.8349 (t80) REVERT: B 1375 ASN cc_start: 0.8122 (p0) cc_final: 0.7778 (p0) REVERT: B 1385 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.6992 (m110) REVERT: B 1392 GLN cc_start: 0.8541 (mt0) cc_final: 0.8201 (mt0) REVERT: C 196 ASP cc_start: 0.8157 (t0) cc_final: 0.7899 (m-30) REVERT: C 197 GLU cc_start: 0.8238 (tp30) cc_final: 0.7973 (tp30) REVERT: C 277 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6346 (mm-30) REVERT: C 281 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 286 ASP cc_start: 0.7530 (t0) cc_final: 0.7281 (t0) REVERT: C 303 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: C 637 THR cc_start: 0.8211 (p) cc_final: 0.7760 (t) REVERT: C 713 THR cc_start: 0.8340 (t) cc_final: 0.8115 (m) REVERT: D 75 TYR cc_start: 0.7850 (t80) cc_final: 0.7581 (t80) REVERT: D 113 GLU cc_start: 0.7834 (tp30) cc_final: 0.7574 (mt-10) REVERT: D 176 GLU cc_start: 0.7980 (tp30) cc_final: 0.7523 (tp30) REVERT: D 202 VAL cc_start: 0.8705 (t) cc_final: 0.8452 (p) REVERT: D 221 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8404 (tpp-160) REVERT: D 272 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7588 (mt-10) REVERT: D 313 MET cc_start: 0.8432 (tpt) cc_final: 0.8127 (tpt) REVERT: D 365 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7608 (tm-30) REVERT: D 427 LEU cc_start: 0.8636 (tp) cc_final: 0.8372 (tt) REVERT: D 448 LEU cc_start: 0.7993 (tp) cc_final: 0.7759 (tm) REVERT: D 452 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 522 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6551 (tppp) REVERT: D 561 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: D 605 ILE cc_start: 0.8613 (mm) cc_final: 0.8352 (mp) REVERT: D 606 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6929 (tm-30) REVERT: D 610 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7892 (mp10) REVERT: D 648 GLU cc_start: 0.7808 (tt0) cc_final: 0.7576 (tt0) REVERT: D 749 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7356 (tt0) REVERT: D 773 LYS cc_start: 0.8426 (tttm) cc_final: 0.8176 (ttmm) REVERT: D 816 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7965 (tt0) REVERT: D 867 GLU cc_start: 0.7458 (tt0) cc_final: 0.7142 (tp30) REVERT: D 926 LEU cc_start: 0.8491 (pp) cc_final: 0.8266 (pt) REVERT: D 935 LYS cc_start: 0.7918 (mttp) cc_final: 0.7605 (mttt) REVERT: D 975 GLU cc_start: 0.7853 (tp30) cc_final: 0.7499 (tp30) REVERT: D 1001 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8186 (mt) REVERT: D 1004 MET cc_start: 0.8014 (mtt) cc_final: 0.7759 (mtp) REVERT: D 1011 LEU cc_start: 0.8159 (mp) cc_final: 0.7897 (mt) REVERT: D 1014 GLU cc_start: 0.8263 (mp0) cc_final: 0.7863 (mp0) REVERT: D 1025 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: D 1049 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7597 (p) outliers start: 66 outliers final: 44 residues processed: 494 average time/residue: 0.7001 time to fit residues: 385.4614 Evaluate side-chains 515 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 459 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1385 ASN Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 351 HIS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 66 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A1075 ASN B1322 ASN B1385 ASN B1393 GLN C 307 ASN D 322 ASN D 634 ASN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 GLN D 946 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119634 restraints weight = 24659.318| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.77 r_work: 0.3286 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18652 Z= 0.251 Angle : 0.706 18.928 25431 Z= 0.361 Chirality : 0.045 0.246 2963 Planarity : 0.004 0.074 2951 Dihedral : 18.551 172.022 3085 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.68 % Allowed : 26.18 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.76 (0.18), residues: 2054 helix: 2.24 (0.14), residues: 1263 sheet: 0.35 (0.38), residues: 185 loop : -0.92 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 178 TYR 0.027 0.002 TYR D 860 PHE 0.027 0.002 PHE A1103 TRP 0.008 0.002 TRP D 589 HIS 0.007 0.001 HIS D 701 Details of bonding type rmsd covalent geometry : bond 0.00596 (18651) covalent geometry : angle 0.70630 (25429) SS BOND : bond 0.00593 ( 1) SS BOND : angle 0.20308 ( 2) hydrogen bonds : bond 0.05118 ( 1115) hydrogen bonds : angle 3.85985 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8879.02 seconds wall clock time: 152 minutes 3.93 seconds (9123.93 seconds total)