Starting phenix.real_space_refine on Sat Jul 4 03:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2x_13783/07_2026/7q2x_13783.map" } 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-dev-6108/lib/python3.11/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: 3.66, per 1000 atoms: 0.20 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: 1.64 Conformation dependent library (CDL) restraints added in 642.2 milliseconds 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: 1.96 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: 4.39 Time building geometry restraints manager: 2.12 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=" C3' DT G 7 " pdb=" C2' DT G 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25196 2.49 - 4.99: 206 4.99 - 7.48: 23 7.48 - 9.97: 2 9.97 - 12.47: 2 Bond angle restraints: 25429 Sorted by residual: angle pdb=" N3 DT G 18 " pdb=" C4 DT G 18 " pdb=" O4 DT G 18 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT G 27 " pdb=" C4 DT G 27 " pdb=" O4 DT G 27 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT G 11 " pdb=" C4 DT G 11 " pdb=" O4 DT G 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT G 12 " pdb=" C4 DT G 12 " pdb=" O4 DT G 12 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT G 16 " pdb=" C4 DT G 16 " pdb=" O4 DT G 16 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (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: 1913 0.032 - 0.063: 709 0.063 - 0.095: 246 0.095 - 0.127: 88 0.127 - 0.159: 7 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: 0.410 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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= 0.387 Angle : 0.636 27.968 25431 Z= 0.404 Chirality : 0.039 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 are 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/Z covalent geometry : bond 0.00306 / 0.23 (18651) covalent geometry : angle 0.58726 / 0.39 (25429) SS BOND : bond 0.84433 / 44.44 ( 1) SS BOND : angle 27.42818 / 15.34 ( 2) hydrogen bonds : bond 0.11821 / 7.74 ( 1115) hydrogen bonds : angle 4.49272 / 3.21 ( 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 : 0.696 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: 0.6584 (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: 0.6024 (tm-30) outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 0.5664 time to fit residues: 279.0177 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 : 0.515 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 106 GLN A 129 GLN B 171 GLN B 266 ASN B 288 ASN B 307 ASN B1322 ASN ** B1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN C 314 GLN 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 417 ASN D 541 HIS ** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.155688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125888 restraints weight = 25045.476| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.85 r_work: 0.3370 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 18652 Z= 0.378 Angle : 0.902 13.198 25431 Z= 0.465 Chirality : 0.054 0.260 2963 Planarity : 0.006 0.087 2951 Dihedral : 18.598 172.181 3085 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.84 % Allowed : 12.04 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2054 helix: 1.61 (0.14), residues: 1281 sheet: 0.94 (0.39), residues: 183 loop : -0.83 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 416 TYR 0.032 0.004 TYR D 529 PHE 0.039 0.004 PHE B 180 TRP 0.018 0.003 TRP A1033 HIS 0.011 0.003 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.38 (18651) covalent geometry : angle 0.90235 / 0.46 (25429) SS BOND : bond 0.04315 / 2.27 ( 1) SS BOND : angle 1.70853 / 0.97 ( 2) hydrogen bonds : bond 0.06249 / 4.14 ( 1115) hydrogen bonds : angle 4.16118 / 2.94 ( 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 596 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 523 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8196 (m-30) cc_final: 0.7960 (m-30) REVERT: A 53 SER cc_start: 0.8105 (t) cc_final: 0.7748 (p) REVERT: A 69 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8059 (mtp180) REVERT: A 71 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8262 (mp-120) REVERT: A 142 ASN cc_start: 0.8533 (t0) cc_final: 0.8248 (t0) REVERT: A 159 SER cc_start: 0.8226 (m) cc_final: 0.7960 (t) REVERT: A 177 ARG cc_start: 0.6790 (ttm-80) cc_final: 0.6583 (tpp-160) REVERT: A 204 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: A 228 GLU cc_start: 0.7052 (mp0) cc_final: 0.6633 (mp0) REVERT: A 983 ASN cc_start: 0.7895 (m-40) cc_final: 0.7682 (t0) REVERT: A 1016 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 1083 GLU cc_start: 0.8096 (pt0) cc_final: 0.7884 (pp20) REVERT: A 1115 ASP cc_start: 0.8546 (p0) cc_final: 0.8270 (p0) REVERT: A 1131 LYS cc_start: 0.8729 (tttp) cc_final: 0.8398 (tttm) REVERT: A 1143 SER cc_start: 0.8583 (p) cc_final: 0.8229 (t) REVERT: B 207 ASN cc_start: 0.7769 (t0) cc_final: 0.7482 (t0) REVERT: B 234 VAL cc_start: 0.8746 (m) cc_final: 0.8509 (t) REVERT: B 264 LYS cc_start: 0.8053 (tppp) cc_final: 0.7829 (tppp) REVERT: B 275 LYS cc_start: 0.7983 (pptt) cc_final: 0.7612 (pptt) REVERT: B 323 LEU cc_start: 0.8387 (tp) cc_final: 0.8099 (tt) REVERT: B 325 GLU cc_start: 0.7756 (mp0) cc_final: 0.7224 (mp0) REVERT: B 328 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7560 (mt-10) REVERT: B 1268 MET cc_start: 0.7929 (mmm) cc_final: 0.7706 (tpp) REVERT: B 1318 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: B 1327 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 1372 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7985 (ttm110) REVERT: C 167 LEU cc_start: 0.7476 (mt) cc_final: 0.7271 (mt) REVERT: C 197 GLU cc_start: 0.8282 (tp30) cc_final: 0.7834 (tp30) REVERT: C 213 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (p) REVERT: C 277 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6911 (mm-30) REVERT: C 281 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8111 (mt) REVERT: C 307 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7143 (m-40) REVERT: C 725 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (t0) REVERT: C 739 ASP cc_start: 0.7919 (t0) cc_final: 0.7679 (t0) REVERT: D 65 LEU cc_start: 0.8150 (mt) cc_final: 0.7865 (mt) REVERT: D 108 TRP cc_start: 0.7362 (OUTLIER) cc_final: 0.7072 (m-10) REVERT: D 202 VAL cc_start: 0.8823 (t) cc_final: 0.8552 (p) REVERT: D 264 GLU cc_start: 0.7592 (mp0) cc_final: 0.7361 (mp0) REVERT: D 287 ASP cc_start: 0.8307 (p0) cc_final: 0.7708 (p0) REVERT: D 313 MET cc_start: 0.8742 (tpt) cc_final: 0.8417 (tpt) REVERT: D 325 ILE cc_start: 0.8760 (mm) cc_final: 0.8466 (mm) REVERT: D 365 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 434 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6073 (pp) REVERT: D 526 MET cc_start: 0.8194 (tpp) cc_final: 0.7975 (mmt) REVERT: D 544 ILE cc_start: 0.7506 (mt) cc_final: 0.7205 (tt) REVERT: D 558 GLU cc_start: 0.8100 (tt0) cc_final: 0.7745 (tt0) REVERT: D 606 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 630 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7841 (tppp) REVERT: D 733 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7993 (m) REVERT: D 748 LEU cc_start: 0.8599 (tp) cc_final: 0.8114 (tt) REVERT: D 751 MET cc_start: 0.6895 (ptm) cc_final: 0.6424 (ptt) REVERT: D 773 LYS cc_start: 0.8467 (tttm) cc_final: 0.8210 (ttmm) REVERT: D 808 ILE cc_start: 0.8247 (mp) cc_final: 0.7907 (mm) REVERT: D 812 ASP cc_start: 0.7965 (m-30) cc_final: 0.7749 (m-30) REVERT: D 816 GLU cc_start: 0.8165 (tt0) cc_final: 0.7803 (tt0) REVERT: D 839 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8324 (mtt90) REVERT: D 964 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7449 (mt-10) REVERT: D 975 GLU cc_start: 0.7992 (tp30) cc_final: 0.7731 (tp30) REVERT: D 982 ILE cc_start: 0.8331 (mm) cc_final: 0.8102 (mp) REVERT: D 1004 MET cc_start: 0.8462 (mtm) cc_final: 0.8046 (mtp) outliers start: 73 outliers final: 18 residues processed: 545 average time/residue: 0.5613 time to fit residues: 342.7754 Evaluate side-chains 504 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 475 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 1016 GLU 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 1292 GLU Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1016 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 168 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN B 288 ASN B1290 ASN C 725 ASN C 738 ASN D 163 GLN D 237 GLN D 555 ASN D 610 GLN D 781 ASN D 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127525 restraints weight = 25085.451| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.84 r_work: 0.3399 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18652 Z= 0.148 Angle : 0.612 9.857 25431 Z= 0.317 Chirality : 0.041 0.218 2963 Planarity : 0.004 0.051 2951 Dihedral : 18.663 179.653 3085 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2054 helix: 2.16 (0.14), residues: 1287 sheet: 1.08 (0.39), residues: 179 loop : -0.75 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 221 TYR 0.021 0.002 TYR D 529 PHE 0.021 0.002 PHE D1149 TRP 0.010 0.001 TRP D 589 HIS 0.007 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18651) covalent geometry : angle 0.61205 / 0.32 (25429) SS BOND : bond 0.00687 / 0.36 ( 1) SS BOND : angle 0.91152 / 0.51 ( 2) hydrogen bonds : bond 0.04482 / 3.02 ( 1115) hydrogen bonds : angle 3.73627 / 2.65 ( 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 559 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 492 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8162 (m-30) cc_final: 0.7922 (m-30) REVERT: A 53 SER cc_start: 0.8042 (t) cc_final: 0.7760 (p) REVERT: A 69 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.7771 (mtp180) REVERT: A 71 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8128 (mp-120) REVERT: A 76 LYS cc_start: 0.8291 (tttp) cc_final: 0.7625 (tttp) REVERT: A 106 GLN cc_start: 0.8117 (mt0) cc_final: 0.7768 (mt0) REVERT: A 107 VAL cc_start: 0.8580 (p) cc_final: 0.8344 (t) REVERT: A 142 ASN cc_start: 0.8498 (t0) cc_final: 0.8262 (t0) REVERT: A 159 SER cc_start: 0.8266 (m) cc_final: 0.7966 (t) REVERT: A 178 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7141 (mtm-85) REVERT: A 1103 PHE cc_start: 0.8560 (t80) cc_final: 0.8201 (t80) REVERT: A 1104 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7947 (ttt180) REVERT: A 1115 ASP cc_start: 0.8523 (p0) cc_final: 0.8302 (p0) REVERT: A 1131 LYS cc_start: 0.8710 (tttp) cc_final: 0.8406 (tttm) REVERT: A 1143 SER cc_start: 0.8493 (p) cc_final: 0.8245 (t) REVERT: B 207 ASN cc_start: 0.7812 (t0) cc_final: 0.7539 (t0) REVERT: B 234 VAL cc_start: 0.8643 (m) cc_final: 0.8425 (t) REVERT: B 275 LYS cc_start: 0.8016 (pptt) cc_final: 0.7741 (pttt) REVERT: B 285 LEU cc_start: 0.7674 (tp) cc_final: 0.7473 (tt) REVERT: B 328 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7523 (mt-10) REVERT: B 331 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7869 (mm) REVERT: B 1321 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 1327 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 1354 ASP cc_start: 0.8391 (p0) cc_final: 0.8171 (p0) REVERT: B 1372 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7946 (ttm110) REVERT: C 70 ILE cc_start: 0.8147 (pt) cc_final: 0.7815 (mp) REVERT: C 197 GLU cc_start: 0.8228 (tp30) cc_final: 0.7859 (tp30) REVERT: C 213 THR cc_start: 0.8706 (p) cc_final: 0.8478 (p) REVERT: C 277 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 281 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (mt) REVERT: C 303 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6509 (tm-30) REVERT: C 739 ASP cc_start: 0.7809 (t0) cc_final: 0.7554 (t0) REVERT: D 62 PHE cc_start: 0.8192 (t80) cc_final: 0.7981 (t80) REVERT: D 65 LEU cc_start: 0.8109 (mt) cc_final: 0.7837 (mt) REVERT: D 175 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8675 (mt) REVERT: D 202 VAL cc_start: 0.8646 (t) cc_final: 0.8377 (p) REVERT: D 264 GLU cc_start: 0.7615 (mp0) cc_final: 0.7388 (mp0) REVERT: D 287 ASP cc_start: 0.8212 (p0) cc_final: 0.7890 (p0) REVERT: D 313 MET cc_start: 0.8681 (tpt) cc_final: 0.8277 (tpt) REVERT: D 365 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 526 MET cc_start: 0.8276 (tpp) cc_final: 0.8034 (mmt) REVERT: D 544 ILE cc_start: 0.7468 (mt) cc_final: 0.7172 (tt) REVERT: D 558 GLU cc_start: 0.8067 (tt0) cc_final: 0.7722 (tt0) REVERT: D 561 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: D 606 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6988 (tm-30) REVERT: D 610 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7938 (mp10) REVERT: D 630 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7846 (tppp) REVERT: D 662 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: D 748 LEU cc_start: 0.8518 (tp) cc_final: 0.7996 (tt) REVERT: D 751 MET cc_start: 0.6887 (ptm) cc_final: 0.6314 (ptp) REVERT: D 773 LYS cc_start: 0.8385 (tttm) cc_final: 0.8121 (ttmm) REVERT: D 791 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8197 (ttp) REVERT: D 812 ASP cc_start: 0.7818 (m-30) cc_final: 0.7592 (m-30) REVERT: D 816 GLU cc_start: 0.8097 (tt0) cc_final: 0.7690 (tt0) REVERT: D 839 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8292 (mtt90) REVERT: D 964 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7055 (mt-10) REVERT: D 975 GLU cc_start: 0.7933 (tp30) cc_final: 0.7721 (tp30) REVERT: D 1004 MET cc_start: 0.8185 (mtm) cc_final: 0.7878 (mtp) REVERT: D 1109 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7875 (ptmm) outliers start: 67 outliers final: 29 residues processed: 519 average time/residue: 0.6190 time to fit residues: 359.3914 Evaluate side-chains 507 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 467 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1170 MET 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 331 ILE Chi-restraints excluded: chain B residue 1309 SER Chi-restraints excluded: chain B residue 1310 VAL 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 B residue 1382 SER Chi-restraints excluded: chain B residue 1408 THR 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 83 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 662 GLN Chi-restraints excluded: chain D residue 733 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1129 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 209 optimal weight: 50.0000 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 132 GLN A1075 ASN B1283 GLN B1393 GLN C 307 ASN C 725 ASN C 738 ASN D 232 GLN D 237 GLN D 371 ASN D 781 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125047 restraints weight = 24978.067| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.82 r_work: 0.3368 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18652 Z= 0.183 Angle : 0.625 12.412 25431 Z= 0.320 Chirality : 0.042 0.241 2963 Planarity : 0.004 0.047 2951 Dihedral : 18.710 177.824 3085 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.68 % Allowed : 19.09 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2054 helix: 2.30 (0.14), residues: 1278 sheet: 0.93 (0.39), residues: 181 loop : -0.76 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 221 TYR 0.024 0.002 TYR D 529 PHE 0.039 0.002 PHE D1149 TRP 0.008 0.001 TRP D 589 HIS 0.006 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (18651) covalent geometry : angle 0.62502 / 0.32 (25429) SS BOND : bond 0.00463 / 0.24 ( 1) SS BOND : angle 0.52914 / 0.31 ( 2) hydrogen bonds : bond 0.04489 / 3.03 ( 1115) hydrogen bonds : angle 3.70215 / 2.61 ( 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 573 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 484 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8179 (t) cc_final: 0.7893 (p) REVERT: A 69 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.7762 (mtp180) REVERT: A 71 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8164 (mp-120) REVERT: A 107 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8384 (t) REVERT: A 142 ASN cc_start: 0.8427 (t0) cc_final: 0.8199 (t0) REVERT: A 159 SER cc_start: 0.8374 (m) cc_final: 0.8032 (p) REVERT: A 210 LEU cc_start: 0.8245 (mt) cc_final: 0.7844 (mt) REVERT: A 1016 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: A 1103 PHE cc_start: 0.8571 (t80) cc_final: 0.8301 (t80) REVERT: A 1104 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7919 (ttt180) REVERT: A 1131 LYS cc_start: 0.8680 (tttp) cc_final: 0.8399 (tttm) REVERT: A 1143 SER cc_start: 0.8500 (p) cc_final: 0.8283 (t) REVERT: B 163 ASN cc_start: 0.8551 (m110) cc_final: 0.8270 (m-40) REVERT: B 207 ASN cc_start: 0.7861 (t0) cc_final: 0.7622 (t0) REVERT: B 210 ARG cc_start: 0.8567 (mtm180) cc_final: 0.8274 (mtm180) REVERT: B 234 VAL cc_start: 0.8660 (m) cc_final: 0.8423 (t) REVERT: B 275 LYS cc_start: 0.8061 (pptt) cc_final: 0.7775 (pttt) REVERT: B 285 LEU cc_start: 0.7741 (tp) cc_final: 0.7522 (tt) REVERT: B 331 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7852 (mm) REVERT: B 1287 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8007 (mtm) REVERT: B 1318 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7871 (mtp85) REVERT: B 1372 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8158 (ttm110) REVERT: C 70 ILE cc_start: 0.8137 (pt) cc_final: 0.7856 (mp) REVERT: C 197 GLU cc_start: 0.8232 (tp30) cc_final: 0.7912 (tp30) REVERT: C 213 THR cc_start: 0.8703 (p) cc_final: 0.8485 (p) REVERT: C 277 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6797 (mm-30) REVERT: C 281 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7981 (mt) REVERT: C 713 THR cc_start: 0.8165 (t) cc_final: 0.7846 (m) REVERT: C 739 ASP cc_start: 0.7812 (t0) cc_final: 0.7576 (t0) REVERT: D 62 PHE cc_start: 0.8223 (t80) cc_final: 0.7995 (t80) REVERT: D 65 LEU cc_start: 0.8102 (mt) cc_final: 0.7860 (mt) REVERT: D 172 THR cc_start: 0.9035 (t) cc_final: 0.8786 (p) REVERT: D 202 VAL cc_start: 0.8676 (t) cc_final: 0.8345 (p) REVERT: D 203 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8239 (tp) REVERT: D 242 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8436 (p) REVERT: D 264 GLU cc_start: 0.7667 (mp0) cc_final: 0.7394 (mp0) REVERT: D 269 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7799 (mm-40) REVERT: D 313 MET cc_start: 0.8624 (tpt) cc_final: 0.8208 (tpt) REVERT: D 325 ILE cc_start: 0.8845 (mm) cc_final: 0.8597 (mm) REVERT: D 349 MET cc_start: 0.7434 (pmm) cc_final: 0.7206 (pmm) REVERT: D 365 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 371 ASN cc_start: 0.8431 (t0) cc_final: 0.8196 (t0) REVERT: D 526 MET cc_start: 0.8206 (tpp) cc_final: 0.7973 (mmt) REVERT: D 558 GLU cc_start: 0.8085 (tt0) cc_final: 0.7788 (tt0) REVERT: D 606 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6998 (tm-30) REVERT: D 610 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7970 (mp10) REVERT: D 630 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7933 (tppp) REVERT: D 662 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: D 748 LEU cc_start: 0.8547 (tp) cc_final: 0.8260 (tp) REVERT: D 751 MET cc_start: 0.6982 (ptm) cc_final: 0.6551 (ptp) REVERT: D 768 GLU cc_start: 0.7504 (tt0) cc_final: 0.7224 (tt0) REVERT: D 773 LYS cc_start: 0.8408 (tttm) cc_final: 0.8127 (ttmm) REVERT: D 812 ASP cc_start: 0.7864 (m-30) cc_final: 0.7627 (m-30) REVERT: D 816 GLU cc_start: 0.8130 (tt0) cc_final: 0.7719 (tt0) REVERT: D 839 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8255 (mtt90) REVERT: D 935 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8063 (mttt) REVERT: D 941 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7918 (mt-10) REVERT: D 964 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7001 (mt-10) REVERT: D 1004 MET cc_start: 0.8205 (mtm) cc_final: 0.7921 (mtp) REVERT: D 1049 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7796 (p) REVERT: D 1109 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (ptmm) outliers start: 89 outliers final: 34 residues processed: 522 average time/residue: 0.5987 time to fit residues: 348.6838 Evaluate side-chains 528 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 480 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 ARG 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 269 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain B residue 1408 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS 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 C residue 708 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 542 LYS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 662 GLN Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 935 LYS 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 1129 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 177 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 132 GLN C 307 ASN C 660 ASN C 725 ASN D 781 ASN D 852 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123316 restraints weight = 24839.793| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.82 r_work: 0.3337 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18652 Z= 0.194 Angle : 0.631 11.429 25431 Z= 0.322 Chirality : 0.043 0.251 2963 Planarity : 0.004 0.048 2951 Dihedral : 18.737 178.032 3085 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.94 % Allowed : 20.14 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2054 helix: 2.29 (0.14), residues: 1271 sheet: 0.83 (0.38), residues: 181 loop : -0.82 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 366 TYR 0.021 0.002 TYR D 529 PHE 0.032 0.002 PHE D1149 TRP 0.009 0.001 TRP D 589 HIS 0.006 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (18651) covalent geometry : angle 0.63061 / 0.32 (25429) SS BOND : bond 0.00315 / 0.17 ( 1) SS BOND : angle 0.40934 / 0.22 ( 2) hydrogen bonds : bond 0.04538 / 3.07 ( 1115) hydrogen bonds : angle 3.69612 / 2.60 ( 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 597 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 503 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8189 (m-30) cc_final: 0.7940 (m-30) REVERT: A 53 SER cc_start: 0.8301 (t) cc_final: 0.8028 (p) REVERT: A 69 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.7655 (mtp180) REVERT: A 71 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8117 (mp-120) REVERT: A 107 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8374 (t) REVERT: A 109 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 159 SER cc_start: 0.8358 (m) cc_final: 0.8022 (p) REVERT: A 195 ASN cc_start: 0.7927 (m-40) cc_final: 0.7620 (m110) REVERT: A 210 LEU cc_start: 0.8189 (mt) cc_final: 0.7936 (mt) REVERT: A 1001 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7970 (mmtp) REVERT: A 1016 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 1029 LEU cc_start: 0.8047 (tm) cc_final: 0.7808 (tt) REVERT: A 1104 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7998 (ttt180) REVERT: A 1131 LYS cc_start: 0.8681 (tttp) cc_final: 0.8396 (tttm) REVERT: A 1143 SER cc_start: 0.8434 (p) cc_final: 0.8221 (t) REVERT: A 1157 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7860 (ttm-80) REVERT: B 163 ASN cc_start: 0.8618 (m110) cc_final: 0.8261 (m-40) REVERT: B 272 ILE cc_start: 0.8170 (pt) cc_final: 0.7917 (mt) REVERT: B 275 LYS cc_start: 0.8073 (pptt) cc_final: 0.7818 (pttt) REVERT: B 331 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7799 (mm) REVERT: B 1268 MET cc_start: 0.8031 (mmm) cc_final: 0.7827 (tpp) REVERT: B 1285 ILE cc_start: 0.8537 (tt) cc_final: 0.8315 (tt) REVERT: B 1287 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: B 1290 ASN cc_start: 0.8418 (m-40) cc_final: 0.8212 (m-40) REVERT: B 1318 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7899 (mtp85) REVERT: B 1360 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7918 (mtp85) REVERT: B 1372 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7921 (ttm110) REVERT: C 70 ILE cc_start: 0.8260 (pt) cc_final: 0.7917 (mp) REVERT: C 196 ASP cc_start: 0.8191 (t0) cc_final: 0.7948 (m-30) REVERT: C 197 GLU cc_start: 0.8279 (tp30) cc_final: 0.7970 (tp30) REVERT: C 211 ASP cc_start: 0.7726 (t0) cc_final: 0.7376 (t0) REVERT: C 213 THR cc_start: 0.8748 (p) cc_final: 0.8540 (p) REVERT: C 277 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6757 (mm-30) REVERT: C 281 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7921 (mt) REVERT: C 661 LEU cc_start: 0.8155 (mt) cc_final: 0.7878 (mp) REVERT: C 713 THR cc_start: 0.8178 (t) cc_final: 0.7910 (m) REVERT: C 739 ASP cc_start: 0.7776 (t0) cc_final: 0.7568 (t0) REVERT: D 62 PHE cc_start: 0.8276 (t80) cc_final: 0.8032 (t80) REVERT: D 65 LEU cc_start: 0.8085 (mt) cc_final: 0.7845 (mt) REVERT: D 195 LEU cc_start: 0.8895 (tt) cc_final: 0.8628 (tp) REVERT: D 203 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8437 (tp) REVERT: D 242 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8401 (p) REVERT: D 264 GLU cc_start: 0.7679 (mp0) cc_final: 0.7362 (mp0) REVERT: D 269 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7766 (mm-40) REVERT: D 313 MET cc_start: 0.8592 (tpt) cc_final: 0.8101 (tpt) REVERT: D 365 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 369 ASP cc_start: 0.7775 (t0) cc_final: 0.7500 (t0) REVERT: D 371 ASN cc_start: 0.8467 (t0) cc_final: 0.8255 (t0) REVERT: D 526 MET cc_start: 0.8166 (tpp) cc_final: 0.7954 (mmt) REVERT: D 544 ILE cc_start: 0.7745 (mt) cc_final: 0.7362 (tt) REVERT: D 558 GLU cc_start: 0.8103 (tt0) cc_final: 0.7720 (tt0) REVERT: D 605 ILE cc_start: 0.8601 (mm) cc_final: 0.8337 (mp) REVERT: D 606 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6995 (tm-30) REVERT: D 610 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7942 (mp10) REVERT: D 662 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: D 736 LYS cc_start: 0.8335 (mmtp) cc_final: 0.8109 (mmmm) REVERT: D 748 LEU cc_start: 0.8527 (tp) cc_final: 0.8213 (tp) REVERT: D 751 MET cc_start: 0.7022 (ptm) cc_final: 0.6656 (ptt) REVERT: D 773 LYS cc_start: 0.8345 (tttm) cc_final: 0.8076 (ttmm) REVERT: D 791 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8195 (ttp) REVERT: D 812 ASP cc_start: 0.7852 (m-30) cc_final: 0.7595 (m-30) REVERT: D 816 GLU cc_start: 0.8100 (tt0) cc_final: 0.7690 (tt0) REVERT: D 926 LEU cc_start: 0.8481 (pp) cc_final: 0.8265 (pt) REVERT: D 935 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (mttt) REVERT: D 941 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7893 (mt-10) REVERT: D 964 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7456 (mt-10) REVERT: D 1004 MET cc_start: 0.8236 (mtm) cc_final: 0.7916 (mtp) REVERT: D 1022 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7301 (tpp-160) REVERT: D 1025 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 1049 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7827 (p) REVERT: D 1109 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7977 (ptmm) outliers start: 94 outliers final: 42 residues processed: 541 average time/residue: 0.6015 time to fit residues: 363.8321 Evaluate side-chains 546 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 486 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 134 VAL 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 1036 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1104 ARG 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 269 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1292 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1372 ARG 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 83 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE 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 203 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 542 LYS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 662 GLN Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 935 LYS 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 1129 GLU 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: 0.8980 chunk 64 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 209 optimal weight: 50.0000 chunk 211 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 106 GLN A 132 GLN A 972 ASN A1075 ASN B 132 ASN C 307 ASN ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN D 781 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 = 0.3858 r_free = 0.3858 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119405 restraints weight = 24570.650| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.83 r_work: 0.3281 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18652 Z= 0.274 Angle : 0.724 11.713 25431 Z= 0.369 Chirality : 0.047 0.257 2963 Planarity : 0.005 0.053 2951 Dihedral : 18.891 175.339 3085 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.05 % Allowed : 20.87 % Favored : 73.08 % 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 are not related in a simple way. whole: 1.59 (0.18), residues: 2054 helix: 2.04 (0.14), residues: 1268 sheet: 0.45 (0.37), residues: 185 loop : -0.91 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 366 TYR 0.028 0.003 TYR D 117 PHE 0.042 0.003 PHE D1149 TRP 0.007 0.002 TRP A1077 HIS 0.014 0.002 HIS D 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.27 (18651) covalent geometry : angle 0.72446 / 0.37 (25429) SS BOND : bond 0.00566 / 0.30 ( 1) SS BOND : angle 0.30672 / 0.18 ( 2) hydrogen bonds : bond 0.05374 / 3.64 ( 1115) hydrogen bonds : angle 3.89838 / 2.74 ( 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 624 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 509 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8345 (t) cc_final: 0.8007 (p) REVERT: A 71 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8130 (mp-120) REVERT: A 107 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8322 (t) REVERT: A 109 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 159 SER cc_start: 0.8395 (m) cc_final: 0.8085 (p) REVERT: A 177 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.6687 (tpt90) REVERT: A 178 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7231 (mtm-85) REVERT: A 189 GLU cc_start: 0.8249 (tp30) cc_final: 0.7846 (tp30) REVERT: A 210 LEU cc_start: 0.8360 (mt) cc_final: 0.7952 (mt) REVERT: A 1001 LYS cc_start: 0.8261 (mmtp) cc_final: 0.8008 (mmtp) REVERT: A 1020 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8087 (mtpt) REVERT: A 1082 ILE cc_start: 0.8661 (pt) cc_final: 0.8366 (mm) REVERT: A 1104 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8055 (ttt180) REVERT: A 1146 GLU cc_start: 0.7888 (tp30) cc_final: 0.7597 (tp30) REVERT: B 179 SER cc_start: 0.8256 (m) cc_final: 0.7752 (t) REVERT: B 234 VAL cc_start: 0.8816 (m) cc_final: 0.8603 (t) REVERT: B 272 ILE cc_start: 0.8487 (pt) cc_final: 0.8247 (mt) REVERT: B 275 LYS cc_start: 0.8267 (pptt) cc_final: 0.7975 (pttt) REVERT: B 304 GLU cc_start: 0.7677 (mp0) cc_final: 0.7235 (mp0) REVERT: B 1268 MET cc_start: 0.8003 (mmm) cc_final: 0.7799 (tpp) REVERT: B 1286 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8166 (p) REVERT: B 1287 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7828 (mtm) REVERT: B 1318 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7934 (mtp85) REVERT: B 1360 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7844 (mtp85) REVERT: B 1372 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7869 (ttm110) REVERT: C 37 MET cc_start: 0.7149 (mtp) cc_final: 0.6851 (mtp) REVERT: C 167 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7110 (mt) REVERT: C 196 ASP cc_start: 0.8209 (t0) cc_final: 0.7956 (m-30) REVERT: C 197 GLU cc_start: 0.8235 (tp30) cc_final: 0.8001 (tp30) REVERT: C 204 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7965 (mp) REVERT: C 211 ASP cc_start: 0.7855 (t0) cc_final: 0.7449 (t0) REVERT: C 277 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6702 (mm-30) REVERT: C 281 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7851 (mt) REVERT: D 62 PHE cc_start: 0.8353 (t80) cc_final: 0.8113 (t80) REVERT: D 203 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8458 (tp) REVERT: D 242 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8413 (p) REVERT: D 264 GLU cc_start: 0.7653 (mp0) cc_final: 0.7333 (mp0) REVERT: D 269 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7794 (mm-40) REVERT: D 313 MET cc_start: 0.8499 (tpt) cc_final: 0.8040 (tpt) REVERT: D 365 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 369 ASP cc_start: 0.8077 (t0) cc_final: 0.7871 (t70) REVERT: D 558 GLU cc_start: 0.8163 (tt0) cc_final: 0.7842 (tt0) REVERT: D 605 ILE cc_start: 0.8671 (mm) cc_final: 0.8412 (mp) REVERT: D 606 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 610 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7968 (mp10) REVERT: D 644 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 736 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8142 (mmmm) REVERT: D 748 LEU cc_start: 0.8529 (tp) cc_final: 0.8095 (tt) REVERT: D 751 MET cc_start: 0.7174 (ptm) cc_final: 0.6825 (ptt) REVERT: D 773 LYS cc_start: 0.8407 (tttm) cc_final: 0.8180 (ttmm) REVERT: D 808 ILE cc_start: 0.8192 (mp) cc_final: 0.7829 (mm) REVERT: D 812 ASP cc_start: 0.7823 (m-30) cc_final: 0.7604 (m-30) REVERT: D 816 GLU cc_start: 0.8119 (tt0) cc_final: 0.7548 (tt0) REVERT: D 861 LEU cc_start: 0.8369 (mt) cc_final: 0.8134 (mp) REVERT: D 926 LEU cc_start: 0.8501 (pp) cc_final: 0.8294 (pt) REVERT: D 941 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7882 (mt-10) REVERT: D 964 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7463 (mt-10) REVERT: D 1004 MET cc_start: 0.8231 (mtt) cc_final: 0.7970 (mtp) REVERT: D 1025 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: D 1049 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7917 (p) REVERT: D 1109 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8066 (ptmm) outliers start: 115 outliers final: 41 residues processed: 563 average time/residue: 0.6299 time to fit residues: 396.6878 Evaluate side-chains 550 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 491 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1104 ARG 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 1318 ARG Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain B residue 1408 THR 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 167 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 637 THR 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 203 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 260 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 793 GLU Chi-restraints excluded: chain D residue 821 THR 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: 1.9990 chunk 147 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 41 optimal weight: 0.0170 chunk 125 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 172 optimal weight: 0.0470 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 132 GLN A 195 ASN A 221 GLN B 132 ASN C 307 ASN C 725 ASN D 178 ASN D 322 ASN D 781 ASN D 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124117 restraints weight = 24876.649| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.79 r_work: 0.3352 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18652 Z= 0.127 Angle : 0.627 12.550 25431 Z= 0.318 Chirality : 0.041 0.240 2963 Planarity : 0.004 0.053 2951 Dihedral : 18.836 178.037 3085 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.84 % Allowed : 24.19 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2054 helix: 2.33 (0.14), residues: 1270 sheet: 0.64 (0.38), residues: 179 loop : -0.87 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 366 TYR 0.022 0.002 TYR D 529 PHE 0.026 0.001 PHE D1149 TRP 0.011 0.001 TRP A1033 HIS 0.006 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (18651) covalent geometry : angle 0.62691 / 0.32 (25429) SS BOND : bond 0.00415 / 0.22 ( 1) SS BOND : angle 0.42972 / 0.25 ( 2) hydrogen bonds : bond 0.04232 / 2.87 ( 1115) hydrogen bonds : angle 3.67618 / 2.59 ( 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 557 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 484 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8182 (m-30) cc_final: 0.7930 (m-30) REVERT: A 53 SER cc_start: 0.8253 (t) cc_final: 0.7951 (p) REVERT: A 69 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7357 (mtp180) REVERT: A 71 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8101 (mp-120) REVERT: A 107 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8291 (t) REVERT: A 109 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 159 SER cc_start: 0.8425 (m) cc_final: 0.8118 (p) REVERT: A 177 ARG cc_start: 0.7235 (tpp-160) cc_final: 0.6522 (tpt90) REVERT: A 185 MET cc_start: 0.8115 (mtp) cc_final: 0.7804 (mtm) REVERT: A 1001 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7943 (mmtp) REVERT: A 1020 LYS cc_start: 0.8242 (ttmm) cc_final: 0.8025 (mtpt) REVERT: A 1104 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7974 (ttt180) REVERT: A 1131 LYS cc_start: 0.8652 (tttt) cc_final: 0.8341 (tttm) REVERT: A 1146 GLU cc_start: 0.7839 (tp30) cc_final: 0.7535 (tp30) REVERT: B 179 SER cc_start: 0.8041 (m) cc_final: 0.7512 (t) REVERT: B 275 LYS cc_start: 0.8149 (pptt) cc_final: 0.7835 (pttt) REVERT: B 285 LEU cc_start: 0.7780 (tp) cc_final: 0.7547 (tt) REVERT: B 304 GLU cc_start: 0.7597 (mp0) cc_final: 0.7203 (mp0) REVERT: B 1295 LEU cc_start: 0.7983 (mm) cc_final: 0.7748 (mp) REVERT: B 1351 ASP cc_start: 0.7863 (t0) cc_final: 0.7566 (t0) REVERT: B 1360 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: B 1372 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7836 (ttm110) REVERT: B 1392 GLN cc_start: 0.8632 (mt0) cc_final: 0.8170 (mt0) REVERT: C 167 LEU cc_start: 0.7086 (tp) cc_final: 0.6886 (mt) REVERT: C 196 ASP cc_start: 0.8191 (t0) cc_final: 0.7926 (m-30) REVERT: C 197 GLU cc_start: 0.8215 (tp30) cc_final: 0.7982 (tp30) REVERT: C 211 ASP cc_start: 0.7862 (t0) cc_final: 0.7448 (t0) REVERT: C 277 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6691 (mm-30) REVERT: C 281 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7818 (mt) REVERT: C 286 ASP cc_start: 0.7501 (t0) cc_final: 0.7248 (t0) REVERT: C 637 THR cc_start: 0.8118 (p) cc_final: 0.7733 (p) REVERT: D 195 LEU cc_start: 0.8802 (tt) cc_final: 0.8560 (tp) REVERT: D 203 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8224 (tp) REVERT: D 242 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (p) REVERT: D 264 GLU cc_start: 0.7650 (mp0) cc_final: 0.7295 (mp0) REVERT: D 269 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7735 (mm-40) REVERT: D 365 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 369 ASP cc_start: 0.7954 (t0) cc_final: 0.7616 (t70) REVERT: D 522 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6819 (tmmm) REVERT: D 558 GLU cc_start: 0.8156 (tt0) cc_final: 0.7810 (tt0) REVERT: D 605 ILE cc_start: 0.8636 (mm) cc_final: 0.8363 (mp) REVERT: D 606 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6935 (tm-30) REVERT: D 610 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7932 (mp10) REVERT: D 644 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8086 (mt) REVERT: D 714 ASP cc_start: 0.7158 (t0) cc_final: 0.6880 (t0) REVERT: D 733 VAL cc_start: 0.8248 (p) cc_final: 0.7999 (m) REVERT: D 736 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8139 (mmmm) REVERT: D 748 LEU cc_start: 0.8404 (tp) cc_final: 0.8131 (tp) REVERT: D 751 MET cc_start: 0.7065 (ptm) cc_final: 0.6750 (ptt) REVERT: D 773 LYS cc_start: 0.8384 (tttm) cc_final: 0.8160 (ttmm) REVERT: D 812 ASP cc_start: 0.7825 (m-30) cc_final: 0.7461 (m-30) REVERT: D 816 GLU cc_start: 0.8097 (tt0) cc_final: 0.7691 (tt0) REVERT: D 941 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7845 (mt-10) REVERT: D 964 GLU cc_start: 0.8095 (mt-10) cc_final: 0.6942 (mt-10) REVERT: D 1014 GLU cc_start: 0.8241 (mp0) cc_final: 0.7691 (mp0) REVERT: D 1025 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: D 1049 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7839 (p) REVERT: D 1109 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (ptmm) outliers start: 73 outliers final: 26 residues processed: 519 average time/residue: 0.6758 time to fit residues: 390.9175 Evaluate side-chains 507 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 468 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL 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 1104 ARG 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 1310 VAL Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain B residue 1412 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR 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: 8.9990 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 132 GLN A1075 ASN B 132 ASN C 307 ASN ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 541 HIS D 781 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122644 restraints weight = 24756.695| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.76 r_work: 0.3328 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18652 Z= 0.171 Angle : 0.648 13.592 25431 Z= 0.327 Chirality : 0.043 0.247 2963 Planarity : 0.004 0.053 2951 Dihedral : 18.840 176.565 3085 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.10 % Allowed : 24.66 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.18), residues: 2054 helix: 2.33 (0.14), residues: 1267 sheet: 0.54 (0.38), residues: 181 loop : -0.91 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 366 TYR 0.031 0.002 TYR B 271 PHE 0.024 0.002 PHE D1149 TRP 0.008 0.001 TRP D 589 HIS 0.005 0.001 HIS D 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (18651) covalent geometry : angle 0.64848 / 0.33 (25429) SS BOND : bond 0.00387 / 0.20 ( 1) SS BOND : angle 0.39504 / 0.21 ( 2) hydrogen bonds : bond 0.04496 / 3.04 ( 1115) hydrogen bonds : angle 3.70443 / 2.61 ( 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 558 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 480 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8364 (t) cc_final: 0.7975 (p) REVERT: A 107 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8324 (t) REVERT: A 109 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 159 SER cc_start: 0.8442 (m) cc_final: 0.8145 (p) REVERT: A 177 ARG cc_start: 0.7308 (tpp-160) cc_final: 0.6624 (tpt90) REVERT: A 178 ARG cc_start: 0.7783 (mtm110) cc_final: 0.7553 (mtm110) REVERT: A 189 GLU cc_start: 0.8167 (tp30) cc_final: 0.7792 (tp30) REVERT: A 210 LEU cc_start: 0.8247 (mt) cc_final: 0.7935 (mt) REVERT: A 1001 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7964 (mmtp) REVERT: A 1003 MET cc_start: 0.8400 (mtp) cc_final: 0.8165 (mtp) REVERT: A 1020 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8047 (mtpt) REVERT: A 1082 ILE cc_start: 0.8666 (pt) cc_final: 0.8417 (mm) REVERT: A 1104 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8511 (ttp80) REVERT: A 1131 LYS cc_start: 0.8677 (tttt) cc_final: 0.8348 (tttm) REVERT: A 1146 GLU cc_start: 0.7872 (tp30) cc_final: 0.7579 (tp30) REVERT: B 179 SER cc_start: 0.8158 (m) cc_final: 0.7646 (t) REVERT: B 275 LYS cc_start: 0.8184 (pptt) cc_final: 0.7852 (pttt) REVERT: B 304 GLU cc_start: 0.7630 (mp0) cc_final: 0.7234 (mp0) REVERT: B 331 ILE cc_start: 0.8180 (mm) cc_final: 0.7752 (mm) REVERT: B 1268 MET cc_start: 0.8056 (mmm) cc_final: 0.7846 (tpp) REVERT: B 1286 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (p) REVERT: B 1287 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7905 (mtm) REVERT: B 1360 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7755 (mtp85) REVERT: B 1372 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (ttm-80) REVERT: B 1392 GLN cc_start: 0.8601 (mt0) cc_final: 0.8139 (mt0) REVERT: C 196 ASP cc_start: 0.8208 (t0) cc_final: 0.7925 (m-30) REVERT: C 197 GLU cc_start: 0.8231 (tp30) cc_final: 0.7997 (tp30) REVERT: C 277 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6672 (mm-30) REVERT: C 281 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7813 (mt) REVERT: C 286 ASP cc_start: 0.7512 (t0) cc_final: 0.7281 (t0) REVERT: C 303 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: C 637 THR cc_start: 0.8140 (p) cc_final: 0.7754 (p) REVERT: D 203 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 242 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8376 (p) REVERT: D 264 GLU cc_start: 0.7666 (mp0) cc_final: 0.7293 (mp0) REVERT: D 269 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7775 (mm-40) REVERT: D 355 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: D 365 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7665 (tm-30) REVERT: D 369 ASP cc_start: 0.7980 (t0) cc_final: 0.7758 (t70) REVERT: D 386 CYS cc_start: 0.8000 (p) cc_final: 0.7658 (m) REVERT: D 427 LEU cc_start: 0.8631 (tp) cc_final: 0.8362 (tt) REVERT: D 558 GLU cc_start: 0.8155 (tt0) cc_final: 0.7852 (tt0) REVERT: D 605 ILE cc_start: 0.8648 (mm) cc_final: 0.8395 (mp) REVERT: D 606 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6963 (tm-30) REVERT: D 610 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7938 (mp10) REVERT: D 644 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (mt) REVERT: D 714 ASP cc_start: 0.7123 (t0) cc_final: 0.6855 (t0) REVERT: D 736 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8157 (mmmm) REVERT: D 748 LEU cc_start: 0.8389 (tp) cc_final: 0.8107 (tp) REVERT: D 773 LYS cc_start: 0.8396 (tttm) cc_final: 0.8162 (ttmm) REVERT: D 812 ASP cc_start: 0.7831 (m-30) cc_final: 0.7488 (m-30) REVERT: D 816 GLU cc_start: 0.8134 (tt0) cc_final: 0.7720 (tt0) REVERT: D 926 LEU cc_start: 0.8496 (pp) cc_final: 0.8269 (pt) REVERT: D 941 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7882 (mt-10) REVERT: D 964 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7062 (mt-10) REVERT: D 1014 GLU cc_start: 0.8242 (mp0) cc_final: 0.7693 (mp0) REVERT: D 1025 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: D 1049 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7830 (p) REVERT: D 1109 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8055 (ptmm) outliers start: 78 outliers final: 41 residues processed: 512 average time/residue: 0.6595 time to fit residues: 375.4679 Evaluate side-chains 531 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 474 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 107 VAL 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 1100 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1104 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 271 TYR 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 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1330 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1370 LYS Chi-restraints excluded: chain B residue 1372 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE 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 203 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 260 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN B 132 ASN B1385 ASN C 292 GLN C 307 ASN C 725 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 781 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123311 restraints weight = 24750.209| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.78 r_work: 0.3349 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18652 Z= 0.133 Angle : 0.633 14.488 25431 Z= 0.319 Chirality : 0.041 0.268 2963 Planarity : 0.004 0.054 2951 Dihedral : 18.844 177.228 3085 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.79 % Allowed : 25.34 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.18), residues: 2054 helix: 2.39 (0.14), residues: 1270 sheet: 0.52 (0.38), residues: 179 loop : -0.94 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 366 TYR 0.025 0.002 TYR B 326 PHE 0.023 0.001 PHE C 170 TRP 0.009 0.001 TRP D 589 HIS 0.007 0.001 HIS D 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (18651) covalent geometry : angle 0.63286 / 0.32 (25429) SS BOND : bond 0.00305 / 0.16 ( 1) SS BOND : angle 0.31027 / 0.17 ( 2) hydrogen bonds : bond 0.04233 / 2.87 ( 1115) hydrogen bonds : angle 3.65818 / 2.58 ( 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: 72 poor density : 469 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8163 (m-30) cc_final: 0.7916 (m-30) REVERT: A 53 SER cc_start: 0.8301 (t) cc_final: 0.7933 (p) REVERT: A 109 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 159 SER cc_start: 0.8420 (m) cc_final: 0.8137 (p) REVERT: A 189 GLU cc_start: 0.8159 (tp30) cc_final: 0.7774 (tp30) REVERT: A 210 LEU cc_start: 0.8218 (mt) cc_final: 0.7851 (mt) REVERT: A 1001 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7961 (mmtp) REVERT: A 1003 MET cc_start: 0.8352 (mtp) cc_final: 0.8116 (mtp) REVERT: A 1020 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8024 (mtpt) REVERT: A 1104 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8487 (ttp80) REVERT: A 1131 LYS cc_start: 0.8673 (tttt) cc_final: 0.8334 (tttm) REVERT: A 1146 GLU cc_start: 0.7867 (tp30) cc_final: 0.7553 (tp30) REVERT: B 179 SER cc_start: 0.8032 (m) cc_final: 0.7515 (t) REVERT: B 275 LYS cc_start: 0.8140 (pptt) cc_final: 0.7837 (pttt) REVERT: B 301 LEU cc_start: 0.7972 (mt) cc_final: 0.7729 (mm) REVERT: B 304 GLU cc_start: 0.7615 (mp0) cc_final: 0.7207 (mp0) REVERT: B 331 ILE cc_start: 0.8160 (mm) cc_final: 0.7728 (mm) REVERT: B 1286 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8131 (p) REVERT: B 1287 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: B 1360 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7747 (mtp85) REVERT: B 1392 GLN cc_start: 0.8605 (mt0) cc_final: 0.8138 (mt0) REVERT: C 70 ILE cc_start: 0.8262 (pt) cc_final: 0.7849 (mp) REVERT: C 196 ASP cc_start: 0.8223 (t0) cc_final: 0.7939 (m-30) REVERT: C 197 GLU cc_start: 0.8208 (tp30) cc_final: 0.7971 (tp30) REVERT: C 277 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6678 (mm-30) REVERT: C 281 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7777 (mt) REVERT: C 286 ASP cc_start: 0.7499 (t0) cc_final: 0.7263 (t0) REVERT: C 303 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: C 637 THR cc_start: 0.8125 (p) cc_final: 0.7735 (p) REVERT: D 195 LEU cc_start: 0.8839 (tt) cc_final: 0.8550 (tp) REVERT: D 242 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 264 GLU cc_start: 0.7679 (mp0) cc_final: 0.7299 (mp0) REVERT: D 355 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: D 365 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7598 (tm-30) REVERT: D 386 CYS cc_start: 0.8000 (p) cc_final: 0.7566 (t) REVERT: D 448 LEU cc_start: 0.8003 (tp) cc_final: 0.7743 (tm) REVERT: D 522 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6617 (tppp) REVERT: D 558 GLU cc_start: 0.8161 (tt0) cc_final: 0.7719 (tt0) REVERT: D 605 ILE cc_start: 0.8624 (mm) cc_final: 0.8363 (mp) REVERT: D 606 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6928 (tm-30) REVERT: D 610 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7918 (mp10) REVERT: D 644 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8079 (mt) REVERT: D 653 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8307 (mtm) REVERT: D 714 ASP cc_start: 0.7199 (t0) cc_final: 0.6935 (t0) REVERT: D 736 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8143 (mmmm) REVERT: D 748 LEU cc_start: 0.8336 (tp) cc_final: 0.8111 (tp) REVERT: D 773 LYS cc_start: 0.8381 (tttm) cc_final: 0.8139 (ttmm) REVERT: D 812 ASP cc_start: 0.7825 (m-30) cc_final: 0.7439 (m-30) REVERT: D 816 GLU cc_start: 0.8129 (tt0) cc_final: 0.7723 (tt0) REVERT: D 926 LEU cc_start: 0.8496 (pp) cc_final: 0.8268 (pt) REVERT: D 941 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7874 (mt-10) REVERT: D 964 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7398 (mt-10) REVERT: D 1014 GLU cc_start: 0.8237 (mp0) cc_final: 0.7674 (mp0) REVERT: D 1049 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7807 (p) REVERT: D 1109 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8041 (ptmm) outliers start: 72 outliers final: 41 residues processed: 503 average time/residue: 0.6440 time to fit residues: 359.9706 Evaluate side-chains 516 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 461 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL 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 1028 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1104 ARG 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 250 ASP Chi-restraints excluded: chain B residue 271 TYR 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 1286 THR Chi-restraints excluded: chain B residue 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 738 ASN 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 203 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 349 MET Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 5.9990 chunk 156 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1075 ASN B 132 ASN B1385 ASN C 307 ASN C 725 ASN D 322 ASN D 781 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124768 restraints weight = 24620.451| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.75 r_work: 0.3364 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18652 Z= 0.128 Angle : 0.642 17.465 25431 Z= 0.324 Chirality : 0.041 0.291 2963 Planarity : 0.004 0.073 2951 Dihedral : 18.833 177.232 3085 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.15 % Allowed : 26.08 % Favored : 70.77 % 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 are not related in a simple way. whole: 1.97 (0.19), residues: 2054 helix: 2.42 (0.14), residues: 1270 sheet: 0.55 (0.39), residues: 179 loop : -0.92 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 178 TYR 0.034 0.002 TYR B 271 PHE 0.022 0.001 PHE C 170 TRP 0.008 0.001 TRP A1033 HIS 0.007 0.001 HIS D 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (18651) covalent geometry : angle 0.64243 / 0.32 (25429) SS BOND : bond 0.00270 / 0.14 ( 1) SS BOND : angle 0.29282 / 0.16 ( 2) hydrogen bonds : bond 0.04123 / 2.79 ( 1115) hydrogen bonds : angle 3.65206 / 2.58 ( 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 525 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 465 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8298 (t) cc_final: 0.7930 (p) REVERT: A 107 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8278 (t) REVERT: A 159 SER cc_start: 0.8432 (m) cc_final: 0.8148 (p) REVERT: A 178 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7059 (mtm-85) REVERT: A 210 LEU cc_start: 0.8182 (mt) cc_final: 0.7887 (mt) REVERT: A 1001 LYS cc_start: 0.8182 (mmtp) cc_final: 0.7982 (mmtp) REVERT: A 1003 MET cc_start: 0.8337 (mtp) cc_final: 0.8079 (mtp) REVERT: A 1020 LYS cc_start: 0.8225 (ttmm) cc_final: 0.8020 (mtpt) REVERT: A 1104 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8475 (ttp80) REVERT: A 1131 LYS cc_start: 0.8678 (tttt) cc_final: 0.8370 (tttm) REVERT: A 1146 GLU cc_start: 0.7870 (tp30) cc_final: 0.7568 (tp30) REVERT: B 275 LYS cc_start: 0.8096 (pptt) cc_final: 0.7782 (pttt) REVERT: B 301 LEU cc_start: 0.7909 (mt) cc_final: 0.7681 (mm) REVERT: B 304 GLU cc_start: 0.7594 (mp0) cc_final: 0.7204 (mp0) REVERT: B 331 ILE cc_start: 0.8151 (mm) cc_final: 0.7714 (mm) REVERT: B 1268 MET cc_start: 0.8040 (tpp) cc_final: 0.6694 (mpp) REVERT: B 1286 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8133 (p) REVERT: B 1287 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7928 (mtm) REVERT: B 1318 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7838 (mtp85) REVERT: B 1351 ASP cc_start: 0.7850 (t0) cc_final: 0.7529 (t0) REVERT: B 1360 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: B 1392 GLN cc_start: 0.8569 (mt0) cc_final: 0.8149 (mt0) REVERT: C 70 ILE cc_start: 0.8276 (pt) cc_final: 0.7863 (mp) REVERT: C 196 ASP cc_start: 0.8196 (t0) cc_final: 0.7905 (m-30) REVERT: C 197 GLU cc_start: 0.8226 (tp30) cc_final: 0.7985 (tp30) REVERT: C 277 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6718 (mm-30) REVERT: C 281 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 286 ASP cc_start: 0.7505 (t0) cc_final: 0.7269 (t0) REVERT: C 303 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: C 637 THR cc_start: 0.8140 (p) cc_final: 0.7750 (p) REVERT: D 195 LEU cc_start: 0.8802 (tt) cc_final: 0.8501 (tp) REVERT: D 264 GLU cc_start: 0.7667 (mp0) cc_final: 0.7296 (mp0) REVERT: D 355 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: D 365 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 386 CYS cc_start: 0.7992 (p) cc_final: 0.7646 (m) REVERT: D 448 LEU cc_start: 0.8019 (tp) cc_final: 0.7774 (tm) REVERT: D 522 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6636 (tppp) REVERT: D 558 GLU cc_start: 0.8150 (tt0) cc_final: 0.7783 (tt0) REVERT: D 605 ILE cc_start: 0.8626 (mm) cc_final: 0.8378 (mp) REVERT: D 606 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6918 (tm-30) REVERT: D 610 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7906 (mp10) REVERT: D 644 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8051 (mt) REVERT: D 653 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8298 (mtm) REVERT: D 736 LYS cc_start: 0.8391 (mmtp) cc_final: 0.8136 (mmmm) REVERT: D 748 LEU cc_start: 0.8339 (tp) cc_final: 0.8115 (tp) REVERT: D 812 ASP cc_start: 0.7818 (m-30) cc_final: 0.7438 (m-30) REVERT: D 816 GLU cc_start: 0.8117 (tt0) cc_final: 0.7721 (tt0) REVERT: D 926 LEU cc_start: 0.8488 (pp) cc_final: 0.8256 (pt) REVERT: D 941 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7849 (mt-10) REVERT: D 964 GLU cc_start: 0.8101 (mt-10) cc_final: 0.6892 (mt-10) REVERT: D 1001 LEU cc_start: 0.8360 (mm) cc_final: 0.8144 (mt) REVERT: D 1014 GLU cc_start: 0.8237 (mp0) cc_final: 0.7659 (mp0) REVERT: D 1049 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7772 (p) REVERT: D 1109 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (ptmm) outliers start: 60 outliers final: 34 residues processed: 495 average time/residue: 0.6163 time to fit residues: 339.6850 Evaluate side-chains 508 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 460 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 271 TYR 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 1318 ARG Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE 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 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 577 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 821 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 66 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 208 optimal weight: 60.0000 chunk 55 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 ASN B1385 ASN C 307 ASN C 725 ASN D 322 ASN D 371 ASN D 634 ASN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 ASN D 946 ASN ** D1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119095 restraints weight = 24786.349| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.87 r_work: 0.3271 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 18652 Z= 0.323 Angle : 0.778 17.339 25431 Z= 0.392 Chirality : 0.049 0.265 2963 Planarity : 0.005 0.072 2951 Dihedral : 18.921 174.931 3085 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.84 % Allowed : 25.55 % Favored : 70.61 % 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 are not related in a simple way. whole: 1.49 (0.18), residues: 2054 helix: 2.07 (0.14), residues: 1264 sheet: 0.21 (0.37), residues: 185 loop : -1.14 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 366 TYR 0.030 0.003 TYR D 117 PHE 0.033 0.003 PHE D 431 TRP 0.010 0.002 TRP C 49 HIS 0.014 0.002 HIS D 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.32 (18651) covalent geometry : angle 0.77780 / 0.39 (25429) SS BOND : bond 0.00654 / 0.34 ( 1) SS BOND : angle 0.27137 / 0.15 ( 2) hydrogen bonds : bond 0.05533 / 3.75 ( 1115) hydrogen bonds : angle 3.94958 / 2.78 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7943.51 seconds wall clock time: 135 minutes 42.90 seconds (8142.90 seconds total)