Starting phenix.real_space_refine on Sat Sep 12 19:38:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q2x_13783/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q2x_13783/09_2026/7q2x_13783.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11373 2.51 5 N 3057 2.21 5 O 3633 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.21, per 1000 atoms: 0.18 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: 1.62 Conformation dependent library (CDL) restraints added in 708.7 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: 1.70 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: 4.07 Time building geometry restraints manager: 2.13 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.290 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: 0.010 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.800 ------------------------------------------------------------------------------- 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 : 0.637 27.968 25431 Z= 0.405 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 0.58829 / 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 : 0.668 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: 0.5750 time to fit residues: 283.6726 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 : 0.526 ------------------------------------------------------------------------------- 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: 5.9990 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 314 GLN C 665 HIS C 725 ASN C 738 ASN D 70 GLN D 83 ASN D 163 GLN D 249 HIS ** 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 = 0.3948 r_free = 0.3948 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126305 restraints weight = 25028.074| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.84 r_work: 0.3378 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.138 18652 Z= 0.384 Angle : 0.895 14.125 25431 Z= 0.461 Chirality : 0.054 0.258 2963 Planarity : 0.006 0.085 2951 Dihedral : 18.548 171.529 3085 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.52 % Allowed : 12.30 % Favored : 84.17 % 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: 1.31 (0.18), residues: 2054 helix: 1.64 (0.14), residues: 1280 sheet: 0.95 (0.39), residues: 183 loop : -0.84 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 416 TYR 0.032 0.004 TYR D 529 PHE 0.040 0.004 PHE B 180 TRP 0.017 0.003 TRP A1077 HIS 0.011 0.003 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.38 (18651) covalent geometry : angle 0.89512 / 0.46 (25429) SS BOND : bond 0.01894 / 1.00 ( 1) SS BOND : angle 1.47404 / 0.85 ( 2) hydrogen bonds : bond 0.06178 / 4.09 ( 1115) hydrogen bonds : angle 4.14784 / 2.93 ( 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 588 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 521 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8181 (m-30) cc_final: 0.7944 (m-30) REVERT: A 53 SER cc_start: 0.8091 (t) cc_final: 0.7734 (p) REVERT: A 69 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8058 (mtp180) REVERT: A 71 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8252 (mp-120) REVERT: A 142 ASN cc_start: 0.8542 (t0) cc_final: 0.8254 (t0) REVERT: A 159 SER cc_start: 0.8219 (m) cc_final: 0.7951 (t) REVERT: A 204 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 228 GLU cc_start: 0.7038 (mp0) cc_final: 0.6665 (mp0) REVERT: A 983 ASN cc_start: 0.7879 (m-40) cc_final: 0.7663 (t0) REVERT: A 1016 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: A 1083 GLU cc_start: 0.8092 (pt0) cc_final: 0.7885 (pp20) REVERT: A 1115 ASP cc_start: 0.8538 (p0) cc_final: 0.8286 (p0) REVERT: A 1131 LYS cc_start: 0.8723 (tttp) cc_final: 0.8392 (tttm) REVERT: A 1143 SER cc_start: 0.8580 (p) cc_final: 0.8225 (t) REVERT: B 207 ASN cc_start: 0.7756 (t0) cc_final: 0.7454 (t0) REVERT: B 234 VAL cc_start: 0.8743 (m) cc_final: 0.8503 (t) REVERT: B 275 LYS cc_start: 0.7964 (pptt) cc_final: 0.7592 (pptt) REVERT: B 323 LEU cc_start: 0.8389 (tp) cc_final: 0.8103 (tt) REVERT: B 325 GLU cc_start: 0.7755 (mp0) cc_final: 0.7222 (mp0) REVERT: B 328 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 1268 MET cc_start: 0.7837 (mmm) cc_final: 0.7622 (tpp) REVERT: B 1318 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: B 1327 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 167 LEU cc_start: 0.7462 (mt) cc_final: 0.7256 (mt) REVERT: C 197 GLU cc_start: 0.8267 (tp30) cc_final: 0.7819 (tp30) REVERT: C 213 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (p) REVERT: C 277 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6885 (mm-30) REVERT: C 281 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 725 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8309 (t0) REVERT: C 739 ASP cc_start: 0.7911 (t0) cc_final: 0.7672 (t0) REVERT: D 65 LEU cc_start: 0.8205 (mt) cc_final: 0.7940 (mt) REVERT: D 108 TRP cc_start: 0.7375 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: D 202 VAL cc_start: 0.8859 (t) cc_final: 0.8581 (p) REVERT: D 264 GLU cc_start: 0.7570 (mp0) cc_final: 0.7356 (mp0) REVERT: D 287 ASP cc_start: 0.8302 (p0) cc_final: 0.7704 (p0) REVERT: D 313 MET cc_start: 0.8747 (tpt) cc_final: 0.8420 (tpt) REVERT: D 325 ILE cc_start: 0.8754 (mm) cc_final: 0.8450 (mm) REVERT: D 365 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 434 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6066 (pp) REVERT: D 526 MET cc_start: 0.8193 (tpp) cc_final: 0.7963 (mmt) REVERT: D 544 ILE cc_start: 0.7488 (mt) cc_final: 0.7266 (tt) REVERT: D 558 GLU cc_start: 0.8093 (tt0) cc_final: 0.7745 (tt0) REVERT: D 606 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 611 LEU cc_start: 0.8427 (mt) cc_final: 0.8223 (mt) REVERT: D 630 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7778 (tppp) REVERT: D 733 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (m) REVERT: D 748 LEU cc_start: 0.8602 (tp) cc_final: 0.8184 (tt) REVERT: D 751 MET cc_start: 0.6874 (ptm) cc_final: 0.6444 (ptp) REVERT: D 773 LYS cc_start: 0.8457 (tttm) cc_final: 0.8184 (ttmm) REVERT: D 808 ILE cc_start: 0.8281 (mp) cc_final: 0.7936 (mm) REVERT: D 812 ASP cc_start: 0.7964 (m-30) cc_final: 0.7723 (m-30) REVERT: D 816 GLU cc_start: 0.8164 (tt0) cc_final: 0.7954 (tt0) REVERT: D 839 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8319 (mtt90) REVERT: D 964 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7452 (mt-10) REVERT: D 975 GLU cc_start: 0.7980 (tp30) cc_final: 0.7717 (tp30) REVERT: D 982 ILE cc_start: 0.8321 (mm) cc_final: 0.8094 (mp) REVERT: D 1004 MET cc_start: 0.8460 (mtm) cc_final: 0.8039 (mtp) outliers start: 67 outliers final: 18 residues processed: 542 average time/residue: 0.5958 time to fit residues: 361.7113 Evaluate side-chains 504 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 477 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 725 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 108 TRP Chi-restraints excluded: chain D residue 118 LEU 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: 7.9990 chunk 141 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 307 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128195 restraints weight = 25089.992| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.82 r_work: 0.3418 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 18652 Z= 0.141 Angle : 0.607 9.486 25431 Z= 0.315 Chirality : 0.041 0.241 2963 Planarity : 0.004 0.049 2951 Dihedral : 18.611 179.443 3085 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.47 % Allowed : 17.98 % Favored : 78.55 % 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: 2.18 (0.14), residues: 1286 sheet: 1.11 (0.39), residues: 179 loop : -0.76 (0.24), residues: 589 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 0.023 0.002 PHE D1149 TRP 0.010 0.001 TRP D 589 HIS 0.006 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (18651) covalent geometry : angle 0.60714 / 0.31 (25429) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 0.87040 / 0.49 ( 2) hydrogen bonds : bond 0.04445 / 3.00 ( 1115) hydrogen bonds : angle 3.72718 / 2.64 ( 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 554 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 488 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8174 (m-30) cc_final: 0.7928 (m-30) REVERT: A 53 SER cc_start: 0.7995 (t) cc_final: 0.7713 (p) REVERT: A 69 ARG cc_start: 0.8498 (mtp-110) cc_final: 0.7776 (mtp180) REVERT: A 71 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8137 (mp-120) REVERT: A 76 LYS cc_start: 0.8273 (tttp) cc_final: 0.7630 (tttp) REVERT: A 106 GLN cc_start: 0.8125 (mt0) cc_final: 0.7793 (mt0) REVERT: A 107 VAL cc_start: 0.8592 (p) cc_final: 0.8353 (t) REVERT: A 142 ASN cc_start: 0.8485 (t0) cc_final: 0.8237 (t0) REVERT: A 159 SER cc_start: 0.8202 (m) cc_final: 0.7904 (t) REVERT: A 178 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7088 (mtm-85) REVERT: A 1103 PHE cc_start: 0.8542 (t80) cc_final: 0.8213 (t80) REVERT: A 1104 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7925 (ttt180) REVERT: A 1115 ASP cc_start: 0.8576 (p0) cc_final: 0.8311 (p0) REVERT: A 1131 LYS cc_start: 0.8679 (tttp) cc_final: 0.8369 (tttm) REVERT: A 1143 SER cc_start: 0.8511 (p) cc_final: 0.8259 (t) REVERT: B 207 ASN cc_start: 0.7793 (t0) cc_final: 0.7513 (t0) REVERT: B 234 VAL cc_start: 0.8642 (m) cc_final: 0.8416 (t) REVERT: B 275 LYS cc_start: 0.7998 (pptt) cc_final: 0.7718 (pttt) REVERT: B 325 GLU cc_start: 0.7712 (mp0) cc_final: 0.7185 (mp0) REVERT: B 328 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 1321 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 1327 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 70 ILE cc_start: 0.8151 (pt) cc_final: 0.7819 (mp) REVERT: C 197 GLU cc_start: 0.8203 (tp30) cc_final: 0.7816 (tp30) REVERT: C 213 THR cc_start: 0.8692 (p) cc_final: 0.8460 (p) REVERT: C 277 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6759 (mm-30) REVERT: C 281 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7915 (mt) REVERT: C 739 ASP cc_start: 0.7812 (t0) cc_final: 0.7551 (t0) REVERT: D 62 PHE cc_start: 0.8181 (t80) cc_final: 0.7978 (t80) REVERT: D 65 LEU cc_start: 0.8099 (mt) cc_final: 0.7831 (mt) REVERT: D 202 VAL cc_start: 0.8659 (t) cc_final: 0.8382 (p) REVERT: D 264 GLU cc_start: 0.7591 (mp0) cc_final: 0.7380 (mp0) REVERT: D 313 MET cc_start: 0.8699 (tpt) cc_final: 0.8288 (tpt) REVERT: D 349 MET cc_start: 0.7413 (pmm) cc_final: 0.7002 (pmm) REVERT: D 365 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 544 ILE cc_start: 0.7402 (mt) cc_final: 0.7132 (tt) REVERT: D 558 GLU cc_start: 0.8056 (tt0) cc_final: 0.7714 (tt0) REVERT: D 561 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: D 606 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6964 (tm-30) REVERT: D 610 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7903 (mp10) REVERT: D 630 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7813 (tppp) REVERT: D 662 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: D 748 LEU cc_start: 0.8533 (tp) cc_final: 0.8009 (tt) REVERT: D 751 MET cc_start: 0.6822 (ptm) cc_final: 0.6277 (ptp) REVERT: D 773 LYS cc_start: 0.8363 (tttm) cc_final: 0.8102 (ttmm) REVERT: D 791 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8170 (ttp) REVERT: D 812 ASP cc_start: 0.7854 (m-30) cc_final: 0.7632 (m-30) REVERT: D 816 GLU cc_start: 0.8072 (tt0) cc_final: 0.7665 (tt0) REVERT: D 822 PHE cc_start: 0.7951 (m-80) cc_final: 0.7744 (m-80) REVERT: D 839 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8303 (mtt90) REVERT: D 964 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7058 (mt-10) REVERT: D 975 GLU cc_start: 0.7924 (tp30) cc_final: 0.7709 (tp30) REVERT: D 983 THR cc_start: 0.8926 (t) cc_final: 0.8687 (p) REVERT: D 1004 MET cc_start: 0.8208 (mtm) cc_final: 0.7884 (mtp) REVERT: D 1109 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7864 (ptmm) outliers start: 66 outliers final: 28 residues processed: 515 average time/residue: 0.5604 time to fit residues: 322.9035 Evaluate side-chains 502 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 466 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 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 C residue 725 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 292 LYS 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 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: 4.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 209 optimal weight: 50.0000 chunk 38 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 132 GLN A1075 ASN B1283 GLN B1385 ASN B1393 GLN C 307 ASN C 725 ASN C 738 ASN D 781 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122662 restraints weight = 24826.912| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.79 r_work: 0.3327 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 18652 Z= 0.293 Angle : 0.717 12.810 25431 Z= 0.369 Chirality : 0.047 0.258 2963 Planarity : 0.005 0.056 2951 Dihedral : 18.767 175.326 3085 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.78 % Allowed : 19.30 % Favored : 75.92 % 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: 1.66 (0.18), residues: 2054 helix: 2.02 (0.14), residues: 1278 sheet: 0.78 (0.39), residues: 179 loop : -0.83 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 366 TYR 0.025 0.003 TYR D 529 PHE 0.026 0.003 PHE D1149 TRP 0.010 0.002 TRP A1077 HIS 0.009 0.002 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.29 (18651) covalent geometry : angle 0.71732 / 0.37 (25429) SS BOND : bond 0.00690 / 0.36 ( 1) SS BOND : angle 0.72669 / 0.43 ( 2) hydrogen bonds : bond 0.05407 / 3.66 ( 1115) hydrogen bonds : angle 3.89602 / 2.74 ( 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 595 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 504 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8308 (t) cc_final: 0.8004 (p) REVERT: A 63 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8320 (tt0) REVERT: A 69 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.7724 (mtp180) REVERT: A 71 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8178 (mp-120) REVERT: A 107 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (t) REVERT: A 159 SER cc_start: 0.8463 (m) cc_final: 0.8168 (t) REVERT: A 178 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7115 (mtm-85) REVERT: A 210 LEU cc_start: 0.8374 (mt) cc_final: 0.7966 (mt) REVERT: A 213 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 1029 LEU cc_start: 0.8113 (tm) cc_final: 0.7870 (tt) REVERT: A 1104 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: A 1131 LYS cc_start: 0.8688 (tttp) cc_final: 0.8375 (tttm) REVERT: B 163 ASN cc_start: 0.8586 (m110) cc_final: 0.8358 (m-40) REVERT: B 207 ASN cc_start: 0.8039 (t0) cc_final: 0.7811 (t0) REVERT: B 234 VAL cc_start: 0.8765 (m) cc_final: 0.8531 (t) REVERT: B 275 LYS cc_start: 0.8171 (pptt) cc_final: 0.7881 (pttt) REVERT: B 285 LEU cc_start: 0.7804 (tp) cc_final: 0.7572 (tt) REVERT: B 323 LEU cc_start: 0.8386 (tp) cc_final: 0.8145 (tt) REVERT: B 1268 MET cc_start: 0.7996 (mmm) cc_final: 0.7787 (tpp) REVERT: B 1287 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7882 (mtm) REVERT: B 1318 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: B 1360 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: C 70 ILE cc_start: 0.8179 (pt) cc_final: 0.7897 (mp) REVERT: C 196 ASP cc_start: 0.8213 (t0) cc_final: 0.7968 (m-30) REVERT: C 197 GLU cc_start: 0.8233 (tp30) cc_final: 0.7957 (tp30) REVERT: C 204 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 277 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6944 (mm-30) REVERT: C 281 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7949 (mt) REVERT: C 303 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6631 (tm-30) REVERT: C 642 SER cc_start: 0.8357 (t) cc_final: 0.8108 (p) REVERT: C 725 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8546 (t0) REVERT: D 62 PHE cc_start: 0.8299 (t80) cc_final: 0.8091 (t80) REVERT: D 65 LEU cc_start: 0.8091 (mt) cc_final: 0.7850 (mt) REVERT: D 202 VAL cc_start: 0.8736 (t) cc_final: 0.8489 (p) REVERT: D 242 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8452 (p) REVERT: D 264 GLU cc_start: 0.7646 (mp0) cc_final: 0.7331 (mp0) REVERT: D 269 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7750 (mm-40) REVERT: D 313 MET cc_start: 0.8609 (tpt) cc_final: 0.8177 (tpt) REVERT: D 349 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7154 (pmm) REVERT: D 365 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7645 (tm-30) REVERT: D 369 ASP cc_start: 0.7755 (t0) cc_final: 0.7480 (t70) REVERT: D 371 ASN cc_start: 0.8508 (t0) cc_final: 0.8147 (t0) REVERT: D 434 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6103 (pp) REVERT: D 526 MET cc_start: 0.8286 (tpp) cc_final: 0.8036 (mmt) REVERT: D 558 GLU cc_start: 0.8075 (tt0) cc_final: 0.7800 (tt0) REVERT: D 605 ILE cc_start: 0.8676 (mm) cc_final: 0.8408 (mp) REVERT: D 606 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7227 (tm-30) REVERT: D 662 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: D 736 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8130 (mmmm) REVERT: D 748 LEU cc_start: 0.8563 (tp) cc_final: 0.8107 (tt) REVERT: D 751 MET cc_start: 0.7046 (ptm) cc_final: 0.6640 (ptt) REVERT: D 768 GLU cc_start: 0.7621 (tt0) cc_final: 0.7377 (tt0) REVERT: D 773 LYS cc_start: 0.8476 (tttm) cc_final: 0.8215 (ttmm) REVERT: D 839 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8327 (mtt90) REVERT: D 871 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6759 (ttm170) REVERT: D 941 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7851 (mt-10) REVERT: D 964 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7546 (mt-10) REVERT: D 1004 MET cc_start: 0.8321 (mtm) cc_final: 0.7976 (mtp) REVERT: D 1049 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7881 (p) REVERT: D 1109 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7957 (ptmm) outliers start: 91 outliers final: 32 residues processed: 540 average time/residue: 0.5813 time to fit residues: 350.9969 Evaluate side-chains 539 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 491 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1036 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1104 ARG Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 299 LEU 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 1408 THR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 725 ASN 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 242 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 434 ILE 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 821 THR Chi-restraints excluded: chain D residue 871 ARG 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: 0.9980 chunk 178 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 94 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 211 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN A 132 GLN A 142 ASN B 211 GLN B1283 GLN C 307 ASN C 660 ASN C 725 ASN ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 ASN D 781 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124704 restraints weight = 24689.709| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.79 r_work: 0.3371 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18652 Z= 0.134 Angle : 0.607 13.218 25431 Z= 0.310 Chirality : 0.041 0.261 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.696 178.290 3085 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.21 % Allowed : 21.92 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2054 helix: 2.32 (0.14), residues: 1272 sheet: 0.78 (0.38), residues: 181 loop : -0.83 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 366 TYR 0.022 0.001 TYR D 529 PHE 0.033 0.001 PHE D1149 TRP 0.010 0.001 TRP D 589 HIS 0.005 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (18651) covalent geometry : angle 0.60680 / 0.31 (25429) SS BOND : bond 0.00286 / 0.15 ( 1) SS BOND : angle 0.41542 / 0.24 ( 2) hydrogen bonds : bond 0.04306 / 2.93 ( 1115) hydrogen bonds : angle 3.66216 / 2.58 ( 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 570 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 490 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8137 (m-30) cc_final: 0.7868 (m-30) REVERT: A 53 SER cc_start: 0.8275 (t) cc_final: 0.7998 (p) REVERT: A 69 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.7715 (mtp180) REVERT: A 71 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8171 (mp-120) REVERT: A 106 GLN cc_start: 0.8139 (mt0) cc_final: 0.7937 (mt0) REVERT: A 107 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 159 SER cc_start: 0.8342 (m) cc_final: 0.8027 (p) REVERT: A 177 ARG cc_start: 0.7019 (tpp-160) cc_final: 0.6576 (ttm170) REVERT: A 210 LEU cc_start: 0.8290 (mt) cc_final: 0.7870 (mt) REVERT: A 1001 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7862 (mmtp) REVERT: A 1029 LEU cc_start: 0.8032 (tm) cc_final: 0.7816 (tt) REVERT: A 1104 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7917 (ttt180) REVERT: A 1131 LYS cc_start: 0.8674 (tttp) cc_final: 0.8443 (tttm) REVERT: A 1157 ARG cc_start: 0.8259 (tpp80) cc_final: 0.8013 (mtp-110) REVERT: B 163 ASN cc_start: 0.8580 (m110) cc_final: 0.8251 (m-40) REVERT: B 207 ASN cc_start: 0.8085 (t0) cc_final: 0.7827 (t0) REVERT: B 272 ILE cc_start: 0.8169 (pt) cc_final: 0.7940 (mt) REVERT: B 275 LYS cc_start: 0.8097 (pptt) cc_final: 0.7833 (pttt) REVERT: B 285 LEU cc_start: 0.7744 (tp) cc_final: 0.7528 (tt) REVERT: B 1268 MET cc_start: 0.8019 (mmm) cc_final: 0.7805 (tpp) REVERT: B 1287 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: B 1318 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7826 (mtp85) REVERT: B 1327 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 1360 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7756 (mtp85) REVERT: C 70 ILE cc_start: 0.8297 (pt) cc_final: 0.7926 (mp) REVERT: C 196 ASP cc_start: 0.8168 (t0) cc_final: 0.7915 (m-30) REVERT: C 197 GLU cc_start: 0.8229 (tp30) cc_final: 0.7939 (tp30) REVERT: C 211 ASP cc_start: 0.7680 (t0) cc_final: 0.7363 (t0) REVERT: C 277 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 281 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (mt) REVERT: C 642 SER cc_start: 0.8294 (t) cc_final: 0.8033 (p) REVERT: C 713 THR cc_start: 0.8143 (t) cc_final: 0.7932 (m) REVERT: C 739 ASP cc_start: 0.7607 (t0) cc_final: 0.7388 (t0) REVERT: C 740 LEU cc_start: 0.8757 (mt) cc_final: 0.8522 (mp) REVERT: D 62 PHE cc_start: 0.8237 (t80) cc_final: 0.8018 (t80) REVERT: D 65 LEU cc_start: 0.8092 (mt) cc_final: 0.7884 (mt) REVERT: D 242 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8370 (p) REVERT: D 264 GLU cc_start: 0.7653 (mp0) cc_final: 0.7331 (mp0) REVERT: D 269 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7720 (mm-40) REVERT: D 324 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (p) REVERT: D 365 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 369 ASP cc_start: 0.7717 (t0) cc_final: 0.7494 (t70) REVERT: D 526 MET cc_start: 0.8226 (tpp) cc_final: 0.7956 (mmt) REVERT: D 544 ILE cc_start: 0.7684 (mt) cc_final: 0.7366 (mt) REVERT: D 548 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7857 (m) REVERT: D 558 GLU cc_start: 0.8088 (tt0) cc_final: 0.7792 (tt0) REVERT: D 606 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 662 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: D 736 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8107 (mmmm) REVERT: D 748 LEU cc_start: 0.8507 (tp) cc_final: 0.8167 (tp) REVERT: D 751 MET cc_start: 0.6964 (ptm) cc_final: 0.6559 (ptt) REVERT: D 816 GLU cc_start: 0.7968 (tt0) cc_final: 0.7741 (tt0) REVERT: D 941 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7846 (mt-10) REVERT: D 964 GLU cc_start: 0.8101 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 1004 MET cc_start: 0.8095 (mtm) cc_final: 0.7853 (mtp) REVERT: D 1025 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: D 1049 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 1109 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8014 (ptmm) outliers start: 80 outliers final: 31 residues processed: 524 average time/residue: 0.6179 time to fit residues: 361.6986 Evaluate side-chains 521 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 477 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1034 GLU 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 299 LEU Chi-restraints excluded: chain B residue 312 LYS 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 1360 ARG Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 172 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 C residue 711 ILE Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 186 THR 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 327 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 662 GLN 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 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: 2.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 209 optimal weight: 50.0000 chunk 211 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN A 132 GLN A 142 ASN A1075 ASN B 132 ASN C 307 ASN C 660 ASN D 781 ASN D 852 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120590 restraints weight = 24606.384| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.81 r_work: 0.3311 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18652 Z= 0.246 Angle : 0.676 12.917 25431 Z= 0.344 Chirality : 0.045 0.269 2963 Planarity : 0.004 0.053 2951 Dihedral : 18.787 175.634 3085 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.05 % Allowed : 21.08 % Favored : 72.87 % 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: 1.76 (0.18), residues: 2054 helix: 2.17 (0.14), residues: 1269 sheet: 0.53 (0.38), residues: 185 loop : -0.85 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 366 TYR 0.023 0.002 TYR D 529 PHE 0.033 0.002 PHE D1149 TRP 0.006 0.002 TRP A1077 HIS 0.009 0.001 HIS D 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (18651) covalent geometry : angle 0.67557 / 0.34 (25429) SS BOND : bond 0.00456 / 0.24 ( 1) SS BOND : angle 0.44978 / 0.25 ( 2) hydrogen bonds : bond 0.05015 / 3.41 ( 1115) hydrogen bonds : angle 3.79296 / 2.67 ( 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 611 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 496 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8358 (t) cc_final: 0.8066 (p) REVERT: A 69 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.7655 (mtp180) REVERT: A 71 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8155 (mp-120) REVERT: A 107 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8401 (t) REVERT: A 129 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6677 (mp-120) REVERT: A 159 SER cc_start: 0.8380 (m) cc_final: 0.8077 (p) REVERT: A 177 ARG cc_start: 0.7178 (tpp-160) cc_final: 0.6523 (tpt90) REVERT: A 178 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7134 (mtm-85) REVERT: A 189 GLU cc_start: 0.8177 (tp30) cc_final: 0.7803 (tp30) REVERT: A 201 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 210 LEU cc_start: 0.8301 (mt) cc_final: 0.7959 (mt) REVERT: A 1001 LYS cc_start: 0.8263 (mmtp) cc_final: 0.8016 (mmtp) REVERT: A 1020 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8117 (mtpt) REVERT: A 1082 ILE cc_start: 0.8664 (pt) cc_final: 0.8446 (mt) REVERT: A 1104 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7998 (ttt180) REVERT: A 1146 GLU cc_start: 0.7912 (tp30) cc_final: 0.7628 (tp30) REVERT: B 163 ASN cc_start: 0.8615 (m110) cc_final: 0.8368 (m-40) REVERT: B 179 SER cc_start: 0.8098 (m) cc_final: 0.7617 (t) REVERT: B 207 ASN cc_start: 0.8148 (t0) cc_final: 0.7923 (t0) REVERT: B 275 LYS cc_start: 0.8200 (pptt) cc_final: 0.7925 (pttt) REVERT: B 285 LEU cc_start: 0.7773 (tp) cc_final: 0.7554 (tt) REVERT: B 323 LEU cc_start: 0.8364 (tp) cc_final: 0.8135 (tt) REVERT: B 1268 MET cc_start: 0.8068 (mmm) cc_final: 0.7856 (tpp) REVERT: B 1287 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7944 (mtm) REVERT: B 1318 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7919 (mtp85) REVERT: B 1360 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7723 (mtp85) REVERT: C 167 LEU cc_start: 0.7271 (mt) cc_final: 0.7050 (tp) REVERT: C 196 ASP cc_start: 0.8187 (t0) cc_final: 0.7945 (m-30) REVERT: C 197 GLU cc_start: 0.8291 (tp30) cc_final: 0.8032 (tp30) REVERT: C 211 ASP cc_start: 0.7782 (t0) cc_final: 0.7426 (t0) REVERT: C 277 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6794 (mm-30) REVERT: C 281 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7889 (mt) REVERT: C 642 SER cc_start: 0.8467 (t) cc_final: 0.8231 (p) REVERT: C 713 THR cc_start: 0.8241 (t) cc_final: 0.7991 (m) REVERT: C 729 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 738 ASN cc_start: 0.8838 (t0) cc_final: 0.8630 (t160) REVERT: C 739 ASP cc_start: 0.7736 (t0) cc_final: 0.7535 (t0) REVERT: C 740 LEU cc_start: 0.8796 (mt) cc_final: 0.8516 (mp) REVERT: D 62 PHE cc_start: 0.8297 (t80) cc_final: 0.8059 (t80) REVERT: D 221 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8404 (tpp80) REVERT: D 225 MET cc_start: 0.8758 (mtm) cc_final: 0.8552 (mtt) REVERT: D 242 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8433 (p) REVERT: D 264 GLU cc_start: 0.7690 (mp0) cc_final: 0.7357 (mp0) REVERT: D 269 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7839 (mm-40) REVERT: D 324 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8438 (p) REVERT: D 365 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 526 MET cc_start: 0.8200 (tpp) cc_final: 0.7932 (mmt) REVERT: D 548 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8081 (m) REVERT: D 558 GLU cc_start: 0.8144 (tt0) cc_final: 0.7833 (tt0) REVERT: D 605 ILE cc_start: 0.8709 (mm) cc_final: 0.8446 (mp) REVERT: D 606 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7236 (tm-30) REVERT: D 644 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8229 (mt) REVERT: D 657 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (mm110) REVERT: D 662 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: D 736 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8197 (mmmm) REVERT: D 748 LEU cc_start: 0.8531 (tp) cc_final: 0.8056 (tt) REVERT: D 769 ASP cc_start: 0.7050 (p0) cc_final: 0.6784 (p0) REVERT: D 773 LYS cc_start: 0.8421 (tttm) cc_final: 0.8197 (ttmm) REVERT: D 819 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7944 (mmm) REVERT: D 861 LEU cc_start: 0.8362 (mt) cc_final: 0.8132 (mp) REVERT: D 941 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7906 (mt-10) REVERT: D 964 GLU cc_start: 0.8158 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 1004 MET cc_start: 0.8221 (mtt) cc_final: 0.7954 (mtp) REVERT: D 1025 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8178 (t0) REVERT: D 1049 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (p) REVERT: D 1109 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (ptmm) outliers start: 115 outliers final: 46 residues processed: 549 average time/residue: 0.6341 time to fit residues: 389.0816 Evaluate side-chains 551 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 486 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 157 LYS 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 1027 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 269 LYS 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 1287 MET Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1318 ARG Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1330 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain B residue 1413 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 315 LEU 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 548 SER Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 657 GLN Chi-restraints excluded: chain D residue 662 GLN Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 819 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 35 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 142 ASN A 972 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122511 restraints weight = 24839.258| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.83 r_work: 0.3345 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18652 Z= 0.146 Angle : 0.632 13.829 25431 Z= 0.320 Chirality : 0.042 0.265 2963 Planarity : 0.004 0.052 2951 Dihedral : 18.789 176.842 3085 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.63 % Allowed : 23.03 % Favored : 72.34 % 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: 2.32 (0.14), residues: 1267 sheet: 0.66 (0.38), residues: 181 loop : -0.85 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1157 TYR 0.026 0.002 TYR B 326 PHE 0.027 0.002 PHE D1149 TRP 0.009 0.001 TRP D 589 HIS 0.004 0.001 HIS D1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (18651) covalent geometry : angle 0.63154 / 0.32 (25429) SS BOND : bond 0.00445 / 0.23 ( 1) SS BOND : angle 0.38868 / 0.21 ( 2) hydrogen bonds : bond 0.04409 / 2.99 ( 1115) hydrogen bonds : angle 3.69494 / 2.60 ( 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 576 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 488 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8275 (t) cc_final: 0.7994 (p) REVERT: A 69 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7623 (mtp180) REVERT: A 71 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8142 (mp-120) REVERT: A 106 GLN cc_start: 0.8174 (mt0) cc_final: 0.7883 (mt0) REVERT: A 107 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8355 (t) REVERT: A 159 SER cc_start: 0.8378 (m) cc_final: 0.8091 (p) REVERT: A 177 ARG cc_start: 0.7170 (tpp-160) cc_final: 0.6528 (tpt90) REVERT: A 178 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7240 (mtm-85) REVERT: A 189 GLU cc_start: 0.8142 (tp30) cc_final: 0.7780 (tp30) REVERT: A 201 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6604 (mm-30) REVERT: A 210 LEU cc_start: 0.8218 (mt) cc_final: 0.7917 (mt) REVERT: A 1001 LYS cc_start: 0.8239 (mmtp) cc_final: 0.8018 (mmtp) REVERT: A 1020 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8089 (mtpt) REVERT: A 1104 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7927 (ttt180) REVERT: A 1131 LYS cc_start: 0.8620 (tttt) cc_final: 0.8331 (tttm) REVERT: A 1146 GLU cc_start: 0.7873 (tp30) cc_final: 0.7581 (tp30) REVERT: B 179 SER cc_start: 0.8035 (m) cc_final: 0.7551 (t) REVERT: B 207 ASN cc_start: 0.8146 (t0) cc_final: 0.7943 (t0) REVERT: B 275 LYS cc_start: 0.8198 (pptt) cc_final: 0.7922 (pttt) REVERT: B 285 LEU cc_start: 0.7784 (tp) cc_final: 0.7559 (tt) REVERT: B 1286 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 1287 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: B 1318 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: B 1360 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7682 (mtp85) REVERT: C 70 ILE cc_start: 0.8291 (pt) cc_final: 0.7912 (mp) REVERT: C 167 LEU cc_start: 0.7161 (mt) cc_final: 0.6902 (tp) REVERT: C 196 ASP cc_start: 0.8186 (t0) cc_final: 0.7929 (m-30) REVERT: C 197 GLU cc_start: 0.8253 (tp30) cc_final: 0.8019 (tp30) REVERT: C 211 ASP cc_start: 0.7773 (t0) cc_final: 0.7390 (t0) REVERT: C 277 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6621 (mm-30) REVERT: C 281 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7875 (mt) REVERT: C 637 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7552 (p) REVERT: C 642 SER cc_start: 0.8375 (t) cc_final: 0.8112 (p) REVERT: C 740 LEU cc_start: 0.8803 (mt) cc_final: 0.8513 (mp) REVERT: D 202 VAL cc_start: 0.8694 (t) cc_final: 0.8412 (p) REVERT: D 221 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8405 (tpp80) REVERT: D 225 MET cc_start: 0.8745 (mtm) cc_final: 0.8532 (mtt) REVERT: D 242 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8369 (p) REVERT: D 264 GLU cc_start: 0.7666 (mp0) cc_final: 0.7324 (mp0) REVERT: D 269 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7768 (mm-40) REVERT: D 324 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8443 (p) REVERT: D 349 MET cc_start: 0.7689 (pmm) cc_final: 0.7241 (pmm) REVERT: D 365 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 522 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6847 (tmmm) REVERT: D 526 MET cc_start: 0.8110 (tpp) cc_final: 0.7855 (mmt) REVERT: D 548 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7940 (m) REVERT: D 558 GLU cc_start: 0.8143 (tt0) cc_final: 0.7831 (tt0) REVERT: D 605 ILE cc_start: 0.8647 (mm) cc_final: 0.8379 (mp) REVERT: D 606 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7197 (tm-30) REVERT: D 644 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8131 (mt) REVERT: D 714 ASP cc_start: 0.7183 (t0) cc_final: 0.6924 (t0) REVERT: D 736 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8173 (mmmm) REVERT: D 748 LEU cc_start: 0.8421 (tp) cc_final: 0.8093 (tp) REVERT: D 773 LYS cc_start: 0.8375 (tttm) cc_final: 0.8144 (ttmm) REVERT: D 816 GLU cc_start: 0.7999 (tt0) cc_final: 0.7760 (tt0) REVERT: D 820 MET cc_start: 0.8618 (mtt) cc_final: 0.8397 (mtm) REVERT: D 941 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7866 (mt-10) REVERT: D 964 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7446 (mt-10) REVERT: D 1004 MET cc_start: 0.8090 (mtt) cc_final: 0.7815 (mtp) REVERT: D 1025 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8165 (t0) REVERT: D 1049 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7859 (p) REVERT: D 1109 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8007 (ptmm) outliers start: 88 outliers final: 39 residues processed: 521 average time/residue: 0.6552 time to fit residues: 380.6643 Evaluate side-chains 531 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 475 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1027 GLU 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 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 1286 THR 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 1413 ASP 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 174 LYS 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 C residue 637 THR Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 522 LYS Chi-restraints excluded: chain D residue 542 LYS Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS 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: 7.9990 chunk 132 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 221 GLN A1075 ASN C 307 ASN C 738 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 = 0.3902 r_free = 0.3902 target = 0.152708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123356 restraints weight = 24745.531| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.80 r_work: 0.3335 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18652 Z= 0.153 Angle : 0.634 16.110 25431 Z= 0.320 Chirality : 0.042 0.264 2963 Planarity : 0.004 0.054 2951 Dihedral : 18.781 176.349 3085 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.15 % Allowed : 24.13 % Favored : 71.71 % 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: 2.36 (0.14), residues: 1267 sheet: 0.63 (0.38), residues: 181 loop : -0.88 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 366 TYR 0.026 0.002 TYR B 326 PHE 0.025 0.002 PHE D1149 TRP 0.009 0.001 TRP D 589 HIS 0.004 0.001 HIS D 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (18651) covalent geometry : angle 0.63397 / 0.32 (25429) SS BOND : bond 0.00301 / 0.16 ( 1) SS BOND : angle 0.44222 / 0.23 ( 2) hydrogen bonds : bond 0.04392 / 2.98 ( 1115) hydrogen bonds : angle 3.67502 / 2.59 ( 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 568 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 489 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8301 (t) cc_final: 0.7973 (p) REVERT: A 69 ARG cc_start: 0.8325 (mtp-110) cc_final: 0.7623 (mtp180) REVERT: A 71 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8139 (mp-120) REVERT: A 107 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8349 (t) REVERT: A 159 SER cc_start: 0.8430 (m) cc_final: 0.8106 (p) REVERT: A 177 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6563 (tpt90) REVERT: A 201 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6600 (mm-30) REVERT: A 210 LEU cc_start: 0.8233 (mt) cc_final: 0.7942 (mt) REVERT: A 1001 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7952 (mmtp) REVERT: A 1003 MET cc_start: 0.8495 (mtp) cc_final: 0.8286 (mtp) REVERT: A 1020 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8109 (mtpt) REVERT: A 1104 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7935 (ttt180) REVERT: A 1131 LYS cc_start: 0.8651 (tttt) cc_final: 0.8325 (tttm) REVERT: A 1146 GLU cc_start: 0.7902 (tp30) cc_final: 0.7608 (tp30) REVERT: B 179 SER cc_start: 0.8030 (m) cc_final: 0.7571 (t) REVERT: B 275 LYS cc_start: 0.8193 (pptt) cc_final: 0.7917 (pttt) REVERT: B 304 GLU cc_start: 0.7649 (mp0) cc_final: 0.7246 (mp0) REVERT: B 1286 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 1287 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: B 1318 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7874 (mtp85) REVERT: B 1360 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7774 (mtp85) REVERT: C 70 ILE cc_start: 0.8286 (pt) cc_final: 0.7891 (mp) REVERT: C 196 ASP cc_start: 0.8190 (t0) cc_final: 0.7917 (m-30) REVERT: C 197 GLU cc_start: 0.8254 (tp30) cc_final: 0.8016 (tp30) REVERT: C 211 ASP cc_start: 0.7797 (t0) cc_final: 0.7405 (t0) REVERT: C 277 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6636 (mm-30) REVERT: C 281 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7873 (mt) REVERT: C 637 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7574 (p) REVERT: C 642 SER cc_start: 0.8363 (t) cc_final: 0.8108 (p) REVERT: D 195 LEU cc_start: 0.8828 (tt) cc_final: 0.8533 (tp) REVERT: D 202 VAL cc_start: 0.8693 (t) cc_final: 0.8430 (p) REVERT: D 242 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8373 (p) REVERT: D 264 GLU cc_start: 0.7697 (mp0) cc_final: 0.7332 (mp0) REVERT: D 269 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7760 (mm-40) REVERT: D 365 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 386 CYS cc_start: 0.8120 (p) cc_final: 0.7599 (t) REVERT: D 526 MET cc_start: 0.8078 (tpp) cc_final: 0.7853 (mmt) REVERT: D 548 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7942 (m) REVERT: D 558 GLU cc_start: 0.8157 (tt0) cc_final: 0.7814 (tt0) REVERT: D 605 ILE cc_start: 0.8654 (mm) cc_final: 0.8392 (mp) REVERT: D 606 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7173 (tm-30) REVERT: D 644 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8135 (mt) REVERT: D 714 ASP cc_start: 0.7143 (t0) cc_final: 0.6879 (t0) REVERT: D 730 LEU cc_start: 0.8487 (mt) cc_final: 0.8216 (mp) REVERT: D 736 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8193 (mmmm) REVERT: D 748 LEU cc_start: 0.8462 (tp) cc_final: 0.8181 (tp) REVERT: D 773 LYS cc_start: 0.8395 (tttm) cc_final: 0.8172 (ttmm) REVERT: D 776 TYR cc_start: 0.8577 (t80) cc_final: 0.8171 (t80) REVERT: D 791 MET cc_start: 0.8432 (tmm) cc_final: 0.8226 (ttp) REVERT: D 816 GLU cc_start: 0.7996 (tt0) cc_final: 0.7622 (tt0) REVERT: D 820 MET cc_start: 0.8615 (mtt) cc_final: 0.8411 (mtm) REVERT: D 926 LEU cc_start: 0.8486 (pp) cc_final: 0.8275 (pt) REVERT: D 941 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7960 (mt-10) REVERT: D 964 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7058 (mt-10) REVERT: D 1004 MET cc_start: 0.8099 (mtt) cc_final: 0.7841 (mtp) REVERT: D 1014 GLU cc_start: 0.8240 (mp0) cc_final: 0.7700 (mp0) REVERT: D 1025 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: D 1049 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7847 (p) REVERT: D 1109 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (ptmm) outliers start: 79 outliers final: 42 residues processed: 517 average time/residue: 0.6303 time to fit residues: 363.3136 Evaluate side-chains 541 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 485 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1027 GLU 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 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 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 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 174 LYS 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 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 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 542 LYS Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS 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: 1.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN B1385 ASN C 292 GLN C 307 ASN D 781 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123832 restraints weight = 24709.435| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.78 r_work: 0.3342 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18652 Z= 0.151 Angle : 0.647 18.049 25431 Z= 0.324 Chirality : 0.042 0.316 2963 Planarity : 0.004 0.066 2951 Dihedral : 18.791 176.309 3085 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.73 % Allowed : 25.13 % Favored : 71.14 % 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: 1.91 (0.18), residues: 2054 helix: 2.33 (0.14), residues: 1273 sheet: 0.55 (0.38), residues: 181 loop : -0.90 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 366 TYR 0.025 0.002 TYR B 326 PHE 0.022 0.002 PHE D 431 TRP 0.008 0.001 TRP D 589 HIS 0.003 0.001 HIS D 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18651) covalent geometry : angle 0.64737 / 0.32 (25429) SS BOND : bond 0.00440 / 0.23 ( 1) SS BOND : angle 0.11354 / 0.06 ( 2) hydrogen bonds : bond 0.04332 / 2.94 ( 1115) hydrogen bonds : angle 3.67234 / 2.59 ( 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 559 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 488 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8157 (t) cc_final: 0.7842 (p) REVERT: A 71 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8155 (mp-120) REVERT: A 107 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 159 SER cc_start: 0.8440 (m) cc_final: 0.8136 (p) REVERT: A 177 ARG cc_start: 0.7184 (tpp-160) cc_final: 0.6526 (tpt90) REVERT: A 178 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7072 (mtm-85) REVERT: A 201 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6626 (mm-30) REVERT: A 210 LEU cc_start: 0.8262 (mt) cc_final: 0.7973 (mt) REVERT: A 1001 LYS cc_start: 0.8284 (mmtp) cc_final: 0.8077 (mmtp) REVERT: A 1003 MET cc_start: 0.8446 (mtp) cc_final: 0.8221 (mtp) REVERT: A 1020 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8072 (mtpt) REVERT: A 1104 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (ttp80) REVERT: A 1131 LYS cc_start: 0.8653 (tttt) cc_final: 0.8314 (tttm) REVERT: A 1146 GLU cc_start: 0.7878 (tp30) cc_final: 0.7580 (tp30) REVERT: B 179 SER cc_start: 0.8031 (m) cc_final: 0.7567 (t) REVERT: B 275 LYS cc_start: 0.8171 (pptt) cc_final: 0.7898 (pttt) REVERT: B 304 GLU cc_start: 0.7639 (mp0) cc_final: 0.7237 (mp0) REVERT: B 1268 MET cc_start: 0.7957 (tpp) cc_final: 0.6754 (mpp) REVERT: B 1286 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 1287 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7963 (mtm) REVERT: B 1360 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7725 (mtp85) REVERT: C 70 ILE cc_start: 0.8290 (pt) cc_final: 0.7900 (mp) REVERT: C 196 ASP cc_start: 0.8203 (t0) cc_final: 0.7923 (m-30) REVERT: C 197 GLU cc_start: 0.8252 (tp30) cc_final: 0.8010 (tp30) REVERT: C 277 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6661 (mm-30) REVERT: C 281 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (mt) REVERT: C 637 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7759 (p) REVERT: D 195 LEU cc_start: 0.8821 (tt) cc_final: 0.8500 (tp) REVERT: D 202 VAL cc_start: 0.8685 (t) cc_final: 0.8452 (p) REVERT: D 242 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8375 (p) REVERT: D 264 GLU cc_start: 0.7691 (mp0) cc_final: 0.7323 (mp0) REVERT: D 269 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7764 (mm-40) REVERT: D 365 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 386 CYS cc_start: 0.8055 (p) cc_final: 0.7619 (t) REVERT: D 427 LEU cc_start: 0.8639 (tp) cc_final: 0.8380 (tt) REVERT: D 548 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7925 (m) REVERT: D 558 GLU cc_start: 0.8185 (tt0) cc_final: 0.7877 (tt0) REVERT: D 605 ILE cc_start: 0.8656 (mm) cc_final: 0.8398 (mp) REVERT: D 606 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 644 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8112 (mt) REVERT: D 714 ASP cc_start: 0.7219 (t0) cc_final: 0.6957 (t0) REVERT: D 730 LEU cc_start: 0.8517 (mt) cc_final: 0.8243 (mp) REVERT: D 736 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8205 (mmmm) REVERT: D 748 LEU cc_start: 0.8459 (tp) cc_final: 0.8206 (tp) REVERT: D 773 LYS cc_start: 0.8418 (tttm) cc_final: 0.8147 (ttmm) REVERT: D 820 MET cc_start: 0.8610 (mtt) cc_final: 0.8379 (mtm) REVERT: D 941 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7938 (mt-10) REVERT: D 964 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7065 (mt-10) REVERT: D 1004 MET cc_start: 0.8078 (mtt) cc_final: 0.7831 (mtp) REVERT: D 1014 GLU cc_start: 0.8213 (mp0) cc_final: 0.7683 (mp0) REVERT: D 1025 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8005 (m-30) REVERT: D 1049 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7831 (p) REVERT: D 1109 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8010 (ptmm) outliers start: 71 outliers final: 42 residues processed: 519 average time/residue: 0.6535 time to fit residues: 378.0931 Evaluate side-chains 535 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 480 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 1027 GLU Chi-restraints excluded: chain A residue 1028 THR 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 250 ASP Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 1246 VAL Chi-restraints excluded: chain B residue 1286 THR 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 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 221 SER 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 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 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 161 optimal weight: 0.0050 chunk 156 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A1075 ASN B1385 ASN C 307 ASN D 322 ASN D 371 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 = 0.3911 r_free = 0.3911 target = 0.153547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124449 restraints weight = 24643.925| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.76 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18652 Z= 0.139 Angle : 0.642 14.321 25431 Z= 0.323 Chirality : 0.043 0.436 2963 Planarity : 0.004 0.054 2951 Dihedral : 18.786 176.325 3085 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.21 % Allowed : 25.87 % Favored : 70.93 % 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: 1.96 (0.19), residues: 2054 helix: 2.39 (0.14), residues: 1272 sheet: 0.56 (0.39), residues: 179 loop : -0.90 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 221 TYR 0.026 0.002 TYR D 117 PHE 0.023 0.002 PHE D 431 TRP 0.009 0.001 TRP D 589 HIS 0.003 0.001 HIS D 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (18651) covalent geometry : angle 0.64180 / 0.32 (25429) SS BOND : bond 0.00284 / 0.15 ( 1) SS BOND : angle 0.32365 / 0.17 ( 2) hydrogen bonds : bond 0.04221 / 2.86 ( 1115) hydrogen bonds : angle 3.67136 / 2.59 ( 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 539 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 478 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 SER cc_start: 0.8142 (t) cc_final: 0.7836 (p) REVERT: A 107 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (t) REVERT: A 159 SER cc_start: 0.8445 (m) cc_final: 0.8153 (p) REVERT: A 177 ARG cc_start: 0.7181 (tpp-160) cc_final: 0.6587 (tpt90) REVERT: A 178 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7454 (mtm110) REVERT: A 201 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6628 (mm-30) REVERT: A 210 LEU cc_start: 0.8257 (mt) cc_final: 0.7939 (mt) REVERT: A 1020 LYS cc_start: 0.8274 (ttmm) cc_final: 0.8055 (mtpt) REVERT: A 1104 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8464 (ttp80) REVERT: A 1131 LYS cc_start: 0.8649 (tttt) cc_final: 0.8354 (tttm) REVERT: A 1146 GLU cc_start: 0.7873 (tp30) cc_final: 0.7575 (tp30) REVERT: B 179 SER cc_start: 0.8003 (m) cc_final: 0.7564 (t) REVERT: B 275 LYS cc_start: 0.8165 (pptt) cc_final: 0.7890 (pttt) REVERT: B 304 GLU cc_start: 0.7632 (mp0) cc_final: 0.7243 (mp0) REVERT: B 1268 MET cc_start: 0.7939 (tpp) cc_final: 0.6760 (mpp) REVERT: B 1286 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 1287 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7971 (mtm) REVERT: B 1360 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: B 1392 GLN cc_start: 0.8496 (mt0) cc_final: 0.8134 (mt0) REVERT: C 70 ILE cc_start: 0.8291 (pt) cc_final: 0.7896 (mp) REVERT: C 196 ASP cc_start: 0.8193 (t0) cc_final: 0.7916 (m-30) REVERT: C 197 GLU cc_start: 0.8228 (tp30) cc_final: 0.7985 (tp30) REVERT: C 277 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6645 (mm-30) REVERT: C 281 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7858 (mt) REVERT: C 637 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7763 (p) REVERT: D 221 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8393 (tpp80) REVERT: D 225 MET cc_start: 0.8772 (mtt) cc_final: 0.8557 (mtm) REVERT: D 242 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8372 (p) REVERT: D 264 GLU cc_start: 0.7674 (mp0) cc_final: 0.7299 (mp0) REVERT: D 269 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7737 (mm-40) REVERT: D 365 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 386 CYS cc_start: 0.8021 (p) cc_final: 0.7606 (t) REVERT: D 427 LEU cc_start: 0.8666 (tp) cc_final: 0.8405 (tt) REVERT: D 448 LEU cc_start: 0.8038 (tp) cc_final: 0.7775 (tm) REVERT: D 548 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7904 (m) REVERT: D 558 GLU cc_start: 0.8169 (tt0) cc_final: 0.7811 (tt0) REVERT: D 605 ILE cc_start: 0.8657 (mm) cc_final: 0.8393 (mp) REVERT: D 606 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7121 (tm-30) REVERT: D 644 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8085 (mt) REVERT: D 714 ASP cc_start: 0.7133 (t0) cc_final: 0.6854 (t0) REVERT: D 730 LEU cc_start: 0.8521 (mt) cc_final: 0.8239 (mp) REVERT: D 736 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8212 (mmmm) REVERT: D 748 LEU cc_start: 0.8451 (tp) cc_final: 0.8212 (tp) REVERT: D 773 LYS cc_start: 0.8419 (tttm) cc_final: 0.8152 (ttmm) REVERT: D 816 GLU cc_start: 0.7985 (tt0) cc_final: 0.7707 (tt0) REVERT: D 941 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7932 (mt-10) REVERT: D 964 GLU cc_start: 0.8118 (mt-10) cc_final: 0.6998 (mt-10) REVERT: D 1004 MET cc_start: 0.8080 (mtt) cc_final: 0.7809 (mtp) REVERT: D 1014 GLU cc_start: 0.8206 (mp0) cc_final: 0.7674 (mp0) REVERT: D 1025 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: D 1049 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7819 (p) REVERT: D 1109 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8002 (ptmm) outliers start: 61 outliers final: 36 residues processed: 504 average time/residue: 0.6248 time to fit residues: 351.1801 Evaluate side-chains 518 residues out of total 1907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 469 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 144 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 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 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 1292 GLU Chi-restraints excluded: chain B residue 1310 VAL Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1360 ARG Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 221 SER 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 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 222 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 724 SER Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 1012 VAL Chi-restraints excluded: chain D residue 1025 ASP Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1109 LYS Chi-restraints excluded: chain D residue 1111 ILE Chi-restraints excluded: chain D residue 1129 GLU Chi-restraints excluded: chain D residue 1150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 66 optimal weight: 10.0000 chunk 210 optimal weight: 10.9990 chunk 208 optimal weight: 60.0000 chunk 55 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN B1385 ASN C 307 ASN C 725 ASN D 781 ASN D 946 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.151049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121749 restraints weight = 24745.255| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.81 r_work: 0.3315 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18652 Z= 0.211 Angle : 0.702 18.071 25431 Z= 0.351 Chirality : 0.044 0.373 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.827 174.947 3085 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.31 % Allowed : 26.03 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.18), residues: 2054 helix: 2.28 (0.14), residues: 1270 sheet: 0.36 (0.37), residues: 183 loop : -0.94 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 366 TYR 0.027 0.002 TYR D 117 PHE 0.029 0.002 PHE D 431 TRP 0.011 0.001 TRP D 108 HIS 0.007 0.001 HIS D 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (18651) covalent geometry : angle 0.70236 / 0.35 (25429) SS BOND : bond 0.00549 / 0.29 ( 1) SS BOND : angle 0.18840 / 0.10 ( 2) hydrogen bonds : bond 0.04870 / 3.31 ( 1115) hydrogen bonds : angle 3.78839 / 2.67 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7944.94 seconds wall clock time: 135 minutes 41.49 seconds (8141.49 seconds total)