Starting phenix.real_space_refine on Tue May 27 09:22:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpk_18555/05_2025/8qpk_18555.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 213 5.49 5 S 44 5.16 5 C 17840 2.51 5 N 5514 2.21 5 O 5916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 2.33s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29527 Number of models: 1 Model: "" Number of chains: 17 Chain: "G" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 658 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 164 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1008 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 251 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 13055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1947, 13055 Classifications: {'peptide': 1947} Incomplete info: {'truncation_to_alanine': 888} Link IDs: {'PTRANS': 106, 'TRANS': 1840} Chain breaks: 1 Unresolved non-hydrogen bonds: 3243 Unresolved non-hydrogen angles: 4104 Unresolved non-hydrogen dihedrals: 2642 Unresolved non-hydrogen chiralities: 277 Planarities with less than four sites: {'GLN:plan1': 56, 'ASP:plan': 88, 'TYR:plan': 24, 'ASN:plan1': 55, 'TRP:plan': 12, 'HIS:plan': 19, 'PHE:plan': 33, 'GLU:plan': 92, 'ARG:plan': 57} Unresolved non-hydrogen planarities: 1875 Chain: "R" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 659 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "U" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2320 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 392} Link IDs: {'PTRANS': 23, 'TRANS': 432} Unresolved non-hydrogen bonds: 1502 Unresolved non-hydrogen angles: 1923 Unresolved non-hydrogen dihedrals: 1262 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 16, 'TYR:plan': 23, 'ASN:plan1': 27, 'TRP:plan': 4, 'ASP:plan': 23, 'PHE:plan': 26, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 853 Chain: "S" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 446 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 5163 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 472} Link IDs: {'PTRANS': 48, 'TRANS': 787} Unresolved non-hydrogen bonds: 1453 Unresolved non-hydrogen angles: 1854 Unresolved non-hydrogen dihedrals: 1114 Unresolved non-hydrogen chiralities: 197 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 51, 'PHE:plan': 8, 'GLU:plan': 49, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 678 Chain: "5" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1620 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 37} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "4" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1617 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 61} Chain breaks: 2 Chain: "X" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 124 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "z" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 239 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "6" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 927 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 22, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 37} Chain breaks: 1 Chain: "N" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 784 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 401 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 127 Chain: "7" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 219 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.05, per 1000 atoms: 0.65 Number of scatterers: 29527 At special positions: 0 Unit cell: (204.16, 140.36, 126.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 213 15.00 O 5916 8.00 N 5514 7.00 C 17840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.16 Conformation dependent library (CDL) restraints added in 4.2 seconds 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7538 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 35 sheets defined 48.8% alpha, 10.0% beta 41 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 10.05 Creating SS restraints... Processing helix chain 'G' and resid 241 through 255 Processing helix chain 'G' and resid 277 through 281 removed outlier: 3.670A pdb=" N GLU G 280 " --> pdb=" O ASP G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 308 through 316 Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 354 removed outlier: 3.502A pdb=" N ASP G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 35 through 52 removed outlier: 3.951A pdb=" N GLU D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.936A pdb=" N PHE D 69 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.547A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 366 Processing helix chain 'L' and resid 368 through 374 removed outlier: 3.615A pdb=" N GLN L 374 " --> pdb=" O GLU L 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.146A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.012A pdb=" N ARG A 82 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS A 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.663A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.808A pdb=" N ALA A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 99 " --> pdb=" O MET A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.092A pdb=" N ASP A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.464A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 4.040A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.694A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 432' Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.691A pdb=" N LYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 590 removed outlier: 6.371A pdb=" N GLY A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 removed outlier: 4.409A pdb=" N TYR A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 3.784A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 removed outlier: 3.863A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 676 through 697 Processing helix chain 'A' and resid 703 through 722 removed outlier: 4.218A pdb=" N ARG A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 804 through 821 Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 887 Processing helix chain 'A' and resid 912 through 933 Processing helix chain 'A' and resid 947 through 962 removed outlier: 3.553A pdb=" N LEU A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 970 removed outlier: 3.510A pdb=" N SER A 969 " --> pdb=" O TRP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.511A pdb=" N LEU A 993 " --> pdb=" O ASP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1014 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.230A pdb=" N HIS A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1117 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.030A pdb=" N GLY A1127 " --> pdb=" O ASN A1124 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A1128 " --> pdb=" O ILE A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1274 through 1281 Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1336 through 1339 Processing helix chain 'A' and resid 1367 through 1372 Processing helix chain 'A' and resid 1374 through 1398 removed outlier: 4.089A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1412 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.982A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 4.170A pdb=" N ARG A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1478 removed outlier: 3.957A pdb=" N THR A1472 " --> pdb=" O ASN A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1486 Processing helix chain 'A' and resid 1487 through 1488 No H-bonds generated for 'chain 'A' and resid 1487 through 1488' Processing helix chain 'A' and resid 1489 through 1493 Processing helix chain 'A' and resid 1507 through 1517 removed outlier: 3.576A pdb=" N LYS A1517 " --> pdb=" O MET A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1528 Processing helix chain 'A' and resid 1528 through 1538 removed outlier: 3.676A pdb=" N ARG A1532 " --> pdb=" O GLN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1615 through 1620 removed outlier: 3.754A pdb=" N SER A1619 " --> pdb=" O PRO A1616 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A1620 " --> pdb=" O ARG A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1654 Processing helix chain 'A' and resid 1675 through 1689 Processing helix chain 'A' and resid 1722 through 1737 Processing helix chain 'A' and resid 1737 through 1751 Processing helix chain 'A' and resid 1764 through 1770 removed outlier: 3.563A pdb=" N GLY A1769 " --> pdb=" O SER A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1787 removed outlier: 3.756A pdb=" N VAL A1785 " --> pdb=" O ASP A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1815 Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1833 through 1852 Processing helix chain 'A' and resid 1865 through 1877 removed outlier: 3.577A pdb=" N ASP A1870 " --> pdb=" O LYS A1866 " (cutoff:3.500A) Proline residue: A1871 - end of helix Processing helix chain 'A' and resid 1893 through 1899 removed outlier: 4.062A pdb=" N LEU A1897 " --> pdb=" O PHE A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1909 Processing helix chain 'A' and resid 1920 through 1926 Processing helix chain 'A' and resid 1928 through 1946 removed outlier: 3.805A pdb=" N PHE A1933 " --> pdb=" O SER A1929 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A1934 " --> pdb=" O TYR A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1946 through 1954 Processing helix chain 'A' and resid 1955 through 1960 Processing helix chain 'A' and resid 1973 through 1994 removed outlier: 3.631A pdb=" N ILE A1977 " --> pdb=" O ASP A1973 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A1982 " --> pdb=" O LYS A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2012 Processing helix chain 'R' and resid 370 through 377 Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 431 through 442 removed outlier: 3.775A pdb=" N ARG R 440 " --> pdb=" O VAL R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 461 through 472 Processing helix chain 'U' and resid 101 through 105 removed outlier: 4.149A pdb=" N CYS U 105 " --> pdb=" O ARG U 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 101 through 105' Processing helix chain 'U' and resid 105 through 111 removed outlier: 4.294A pdb=" N ASP U 109 " --> pdb=" O CYS U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 183 through 186 removed outlier: 3.543A pdb=" N LEU U 186 " --> pdb=" O ASP U 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 183 through 186' Processing helix chain 'U' and resid 187 through 194 Processing helix chain 'U' and resid 198 through 207 removed outlier: 3.555A pdb=" N ASN U 204 " --> pdb=" O GLN U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 245 removed outlier: 3.608A pdb=" N ASN U 237 " --> pdb=" O ASN U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 246 through 255 Processing helix chain 'U' and resid 255 through 262 removed outlier: 4.047A pdb=" N ILE U 262 " --> pdb=" O ASN U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 269 through 286 Processing helix chain 'U' and resid 296 through 307 Processing helix chain 'U' and resid 318 through 335 Processing helix chain 'U' and resid 343 through 349 removed outlier: 3.629A pdb=" N PHE U 349 " --> pdb=" O VAL U 345 " (cutoff:3.500A) Processing helix chain 'U' and resid 366 through 376 Processing helix chain 'U' and resid 415 through 420 Processing helix chain 'U' and resid 479 through 485 Processing helix chain 'U' and resid 486 through 490 removed outlier: 3.542A pdb=" N ALA U 490 " --> pdb=" O GLU U 487 " (cutoff:3.500A) Processing helix chain 'S' and resid 721 through 735 Processing helix chain 'S' and resid 739 through 759 Processing helix chain 'S' and resid 767 through 776 removed outlier: 3.786A pdb=" N GLN S 776 " --> pdb=" O LEU S 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 removed outlier: 3.597A pdb=" N MET C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 removed outlier: 3.771A pdb=" N LYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.672A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.108A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.987A pdb=" N ILE C 299 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 removed outlier: 3.611A pdb=" N LEU C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 411 through 424 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.547A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.810A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 468 Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 removed outlier: 3.568A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.709A pdb=" N ASP C 699 " --> pdb=" O GLY C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 736 through 740 removed outlier: 3.627A pdb=" N ALA C 739 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 762 removed outlier: 4.559A pdb=" N LEU C 758 " --> pdb=" O VAL C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 776 Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 804 through 807 Processing helix chain 'C' and resid 808 through 823 Processing helix chain 'C' and resid 842 through 853 Processing helix chain 'C' and resid 877 through 881 removed outlier: 3.786A pdb=" N PHE C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 877 through 881' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'N' and resid 18 through 24 removed outlier: 3.839A pdb=" N GLY N 24 " --> pdb=" O GLY N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 114 Processing helix chain 'N' and resid 116 through 135 removed outlier: 3.620A pdb=" N GLU N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 141 Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.096A pdb=" N ALA N 150 " --> pdb=" O LYS N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 159 removed outlier: 3.863A pdb=" N TRP N 157 " --> pdb=" O THR N 153 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 259 removed outlier: 3.949A pdb=" N GLY N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 262 No H-bonds generated for 'chain 'N' and resid 260 through 262' Processing helix chain 'B' and resid 46 through 50 removed outlier: 4.032A pdb=" N THR B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 83 Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.261A pdb=" N ASN B 202 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 473 Processing sheet with id=AA1, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.524A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL D 61 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG D 29 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.524A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL D 61 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG D 29 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 26 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 91 through 93 removed outlier: 5.872A pdb=" N MET D 91 " --> pdb=" O VAL D 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 377 through 379 Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.980A pdb=" N ARG A 419 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA8, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA9, first strand: chain 'A' and resid 905 through 910 Processing sheet with id=AB1, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 6.673A pdb=" N PHE A1098 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A1088 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS A1096 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A1090 " --> pdb=" O ARG A1094 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A1094 " --> pdb=" O ARG A1090 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1185 through 1187 Processing sheet with id=AB3, first strand: chain 'A' and resid 1341 through 1345 Processing sheet with id=AB4, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AB5, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 8.480A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1638 through 1639 Processing sheet with id=AB7, first strand: chain 'A' and resid 1777 through 1778 removed outlier: 3.649A pdb=" N TRP A1778 " --> pdb=" O GLN A1860 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1788 through 1790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1817 through 1819 removed outlier: 3.806A pdb=" N PHE A1917 " --> pdb=" O LEU A1817 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1819 " --> pdb=" O VAL A1915 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 412 through 414 removed outlier: 5.013A pdb=" N TYR R 424 " --> pdb=" O ILE R 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 142 through 143 Processing sheet with id=AC3, first strand: chain 'U' and resid 352 through 353 Processing sheet with id=AC4, first strand: chain 'U' and resid 356 through 358 Processing sheet with id=AC5, first strand: chain 'U' and resid 449 through 453 removed outlier: 6.004A pdb=" N ALA U 547 " --> pdb=" O HIS U 505 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N HIS U 505 " --> pdb=" O ALA U 547 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS U 553 " --> pdb=" O LEU U 499 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU U 499 " --> pdb=" O LYS U 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 457 through 459 Processing sheet with id=AC7, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AC8, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.866A pdb=" N ARG C 130 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 201 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY C 224 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 228 through 230 removed outlier: 6.130A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AD2, first strand: chain 'C' and resid 522 through 526 removed outlier: 3.803A pdb=" N GLN C 523 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS C 477 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL C 496 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 479 " --> pdb=" O GLY C 494 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY C 494 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET C 481 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA C 492 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER C 483 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE C 490 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.896A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.896A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.415A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.782A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 674 through 678 removed outlier: 6.916A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) 1427 hydrogen bonds defined for protein. 4095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 17.83 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7550 1.33 - 1.45: 6775 1.45 - 1.57: 15784 1.57 - 1.69: 413 1.69 - 1.81: 71 Bond restraints: 30593 Sorted by residual: bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.603 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 IHP A2401 " pdb=" O15 IHP A2401 " ideal model delta sigma weight residual 1.389 1.457 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.609 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 IHP A2401 " pdb=" O11 IHP A2401 " ideal model delta sigma weight residual 1.392 1.451 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" C3 IHP A2401 " pdb=" O13 IHP A2401 " ideal model delta sigma weight residual 1.393 1.447 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 30588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 42778 2.64 - 5.28: 253 5.28 - 7.93: 18 7.93 - 10.57: 2 10.57 - 13.21: 3 Bond angle restraints: 43054 Sorted by residual: angle pdb=" C LYS A 85 " pdb=" CA LYS A 85 " pdb=" CB LYS A 85 " ideal model delta sigma weight residual 116.54 109.75 6.79 1.15e+00 7.56e-01 3.49e+01 angle pdb=" C1 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" C5 IHP A2401 " ideal model delta sigma weight residual 108.26 121.47 -13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C3 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C5 IHP A2401 " ideal model delta sigma weight residual 107.91 120.01 -12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C3 IHP A2401 " ideal model delta sigma weight residual 108.51 120.50 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 110.39 116.30 -5.91 1.66e+00 3.63e-01 1.27e+01 ... (remaining 43049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17539 35.78 - 71.55: 634 71.55 - 107.33: 62 107.33 - 143.10: 2 143.10 - 178.88: 7 Dihedral angle restraints: 18244 sinusoidal: 6655 harmonic: 11589 Sorted by residual: dihedral pdb=" O4' U z 6 " pdb=" C1' U z 6 " pdb=" N1 U z 6 " pdb=" C2 U z 6 " ideal model delta sinusoidal sigma weight residual 200.00 36.92 163.08 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual -128.00 50.88 -178.88 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 5 78 " pdb=" C1' U 5 78 " pdb=" N1 U 5 78 " pdb=" C2 U 5 78 " ideal model delta sinusoidal sigma weight residual -128.00 48.06 -176.06 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 18241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.978: 5209 0.978 - 1.957: 0 1.957 - 2.935: 0 2.935 - 3.913: 0 3.913 - 4.892: 4 Chirality restraints: 5213 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.37 -4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.25 -4.67 2.00e-01 2.50e+01 5.44e+02 chirality pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O11 IHP A2401 " both_signs ideal model delta sigma weight residual False 2.32 -2.28 4.60 2.00e-01 2.50e+01 5.29e+02 ... (remaining 5210 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 463 " 0.069 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 464 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1263 " 0.018 2.00e-02 2.50e+03 1.63e-02 6.61e+00 pdb=" CG TRP A1263 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A1263 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A1263 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1263 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1263 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1263 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1263 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1263 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1263 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 910 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO C 911 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 911 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 911 " -0.031 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3382 2.75 - 3.29: 30113 3.29 - 3.82: 52468 3.82 - 4.36: 54004 4.36 - 4.90: 88097 Nonbonded interactions: 228064 Sorted by model distance: nonbonded pdb=" O PHE A 540 " pdb=" O2' A z -3 " model vdw 2.209 3.040 nonbonded pdb=" O PHE A1684 " pdb=" OG1 THR A1688 " model vdw 2.220 3.040 nonbonded pdb=" O TRP A 966 " pdb=" OH TYR A1178 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 223 " pdb=" O5' U 5 12 " model vdw 2.241 3.040 nonbonded pdb=" O CYS A1190 " pdb=" OH TYR A1273 " model vdw 2.243 3.040 ... (remaining 228059 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.930 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: 0.000 Extract box with map and model: 0.540 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 78.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 30593 Z= 0.119 Angle : 0.494 13.209 43054 Z= 0.257 Chirality : 0.135 4.892 5213 Planarity : 0.004 0.107 4992 Dihedral : 17.282 178.878 10706 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3936 helix: 2.13 (0.13), residues: 1679 sheet: -1.26 (0.25), residues: 411 loop : -0.27 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1263 HIS 0.016 0.001 HIS G 248 PHE 0.019 0.001 PHE A 230 TYR 0.026 0.001 TYR A1044 ARG 0.007 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.17807 ( 1503) hydrogen bonds : angle 6.22551 ( 4235) covalent geometry : bond 0.00228 (30593) covalent geometry : angle 0.49359 (43054) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8187 (tmm) cc_final: 0.7981 (tmm) REVERT: A 1292 GLU cc_start: 0.7460 (tp30) cc_final: 0.7094 (tp30) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.3407 time to fit residues: 139.7164 Evaluate side-chains 201 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.078347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060818 restraints weight = 165829.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062141 restraints weight = 96856.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063072 restraints weight = 66418.866| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30593 Z= 0.280 Angle : 0.662 18.047 43054 Z= 0.343 Chirality : 0.043 0.455 5213 Planarity : 0.005 0.064 4992 Dihedral : 17.324 174.910 7376 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.14 % Allowed : 6.82 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3936 helix: 1.43 (0.12), residues: 1752 sheet: -1.58 (0.25), residues: 403 loop : -0.67 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 966 HIS 0.016 0.002 HIS G 248 PHE 0.022 0.002 PHE A 387 TYR 0.023 0.002 TYR A 928 ARG 0.005 0.001 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 1503) hydrogen bonds : angle 5.13885 ( 4235) covalent geometry : bond 0.00571 (30593) covalent geometry : angle 0.66231 (43054) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9310 (mm) cc_final: 0.9011 (pp) REVERT: A 789 GLU cc_start: 0.8690 (mp0) cc_final: 0.8202 (mp0) REVERT: A 902 TYR cc_start: 0.8197 (m-80) cc_final: 0.7948 (m-80) REVERT: A 1292 GLU cc_start: 0.7583 (tp30) cc_final: 0.7083 (tp30) REVERT: S 729 LEU cc_start: 0.9269 (mt) cc_final: 0.9043 (mt) REVERT: S 733 PHE cc_start: 0.8442 (m-10) cc_final: 0.8228 (m-10) outliers start: 2 outliers final: 1 residues processed: 219 average time/residue: 0.3510 time to fit residues: 131.6713 Evaluate side-chains 191 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 155 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 358 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 176 optimal weight: 0.0770 chunk 392 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.081445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063887 restraints weight = 164107.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065307 restraints weight = 95613.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.066248 restraints weight = 65347.162| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30593 Z= 0.109 Angle : 0.504 8.556 43054 Z= 0.258 Chirality : 0.040 0.388 5213 Planarity : 0.004 0.055 4992 Dihedral : 17.208 178.135 7376 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3936 helix: 1.88 (0.12), residues: 1739 sheet: -1.37 (0.26), residues: 378 loop : -0.53 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 939 HIS 0.007 0.001 HIS A 755 PHE 0.015 0.001 PHE A 681 TYR 0.023 0.001 TYR A 394 ARG 0.012 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1503) hydrogen bonds : angle 4.50292 ( 4235) covalent geometry : bond 0.00222 (30593) covalent geometry : angle 0.50358 (43054) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9299 (mm) cc_final: 0.8953 (pp) REVERT: A 789 GLU cc_start: 0.8611 (mp0) cc_final: 0.8203 (mp0) REVERT: A 966 TRP cc_start: 0.8387 (m100) cc_final: 0.8122 (m100) REVERT: A 1292 GLU cc_start: 0.7514 (tp30) cc_final: 0.7158 (tp30) REVERT: R 413 ILE cc_start: 0.7741 (pt) cc_final: 0.7527 (pt) REVERT: S 729 LEU cc_start: 0.9171 (mt) cc_final: 0.8912 (mt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3863 time to fit residues: 161.4405 Evaluate side-chains 197 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 392 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 105 optimal weight: 0.0870 chunk 249 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 407 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 771 GLN ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.077548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060300 restraints weight = 171565.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061579 restraints weight = 102090.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.062463 restraints weight = 70828.514| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 30593 Z= 0.324 Angle : 0.680 9.163 43054 Z= 0.365 Chirality : 0.045 0.450 5213 Planarity : 0.005 0.067 4992 Dihedral : 17.486 172.535 7376 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3936 helix: 1.05 (0.12), residues: 1740 sheet: -1.81 (0.24), residues: 408 loop : -0.93 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 709 HIS 0.015 0.002 HIS G 248 PHE 0.024 0.002 PHE A 207 TYR 0.025 0.003 TYR X 140 ARG 0.007 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 1503) hydrogen bonds : angle 5.24256 ( 4235) covalent geometry : bond 0.00658 (30593) covalent geometry : angle 0.67964 (43054) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 276 TRP cc_start: 0.8627 (m100) cc_final: 0.8422 (m100) REVERT: G 340 LEU cc_start: 0.9357 (mm) cc_final: 0.9035 (pp) REVERT: A 95 MET cc_start: 0.8341 (tpp) cc_final: 0.8112 (tpp) REVERT: A 789 GLU cc_start: 0.8540 (mp0) cc_final: 0.8149 (mp0) REVERT: A 902 TYR cc_start: 0.8144 (m-80) cc_final: 0.7805 (m-80) REVERT: S 729 LEU cc_start: 0.9234 (mt) cc_final: 0.8934 (mt) REVERT: S 733 PHE cc_start: 0.8353 (m-10) cc_final: 0.8120 (m-10) REVERT: C 481 MET cc_start: 0.8250 (tpp) cc_final: 0.8002 (tpt) REVERT: C 599 GLU cc_start: 0.8448 (mp0) cc_final: 0.8070 (mp0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3384 time to fit residues: 129.4181 Evaluate side-chains 185 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 124 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 407 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.078767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061380 restraints weight = 169442.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062704 restraints weight = 100362.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063613 restraints weight = 69040.212| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30593 Z= 0.209 Angle : 0.583 10.259 43054 Z= 0.306 Chirality : 0.042 0.399 5213 Planarity : 0.004 0.063 4992 Dihedral : 17.474 174.127 7376 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3936 helix: 1.22 (0.12), residues: 1733 sheet: -1.77 (0.25), residues: 387 loop : -0.93 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1263 HIS 0.009 0.001 HIS C 642 PHE 0.024 0.002 PHE A 207 TYR 0.017 0.002 TYR A1091 ARG 0.010 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1503) hydrogen bonds : angle 4.95332 ( 4235) covalent geometry : bond 0.00432 (30593) covalent geometry : angle 0.58266 (43054) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 294 HIS cc_start: 0.8853 (t-90) cc_final: 0.8611 (t-90) REVERT: G 340 LEU cc_start: 0.9272 (mm) cc_final: 0.9003 (pp) REVERT: A 95 MET cc_start: 0.8407 (tpp) cc_final: 0.8065 (tpp) REVERT: A 902 TYR cc_start: 0.7947 (m-80) cc_final: 0.7500 (m-80) REVERT: A 966 TRP cc_start: 0.8510 (m100) cc_final: 0.8187 (m100) REVERT: S 729 LEU cc_start: 0.9259 (mt) cc_final: 0.8960 (mt) REVERT: S 733 PHE cc_start: 0.8414 (m-10) cc_final: 0.8136 (m-10) REVERT: C 481 MET cc_start: 0.8269 (tpp) cc_final: 0.7986 (tpt) REVERT: C 599 GLU cc_start: 0.8535 (mp0) cc_final: 0.8052 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3407 time to fit residues: 132.7588 Evaluate side-chains 193 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 182 optimal weight: 9.9990 chunk 316 optimal weight: 0.6980 chunk 318 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 390 optimal weight: 0.0030 chunk 350 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 396 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS A 994 ASN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063281 restraints weight = 162304.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064714 restraints weight = 93450.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065679 restraints weight = 63230.399| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30593 Z= 0.104 Angle : 0.509 8.647 43054 Z= 0.260 Chirality : 0.040 0.334 5213 Planarity : 0.004 0.057 4992 Dihedral : 17.294 178.473 7376 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3936 helix: 1.77 (0.13), residues: 1738 sheet: -1.54 (0.26), residues: 379 loop : -0.69 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 206 HIS 0.014 0.001 HIS G 248 PHE 0.016 0.001 PHE A 681 TYR 0.030 0.001 TYR A 454 ARG 0.017 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1503) hydrogen bonds : angle 4.38554 ( 4235) covalent geometry : bond 0.00220 (30593) covalent geometry : angle 0.50933 (43054) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 294 HIS cc_start: 0.8842 (t-90) cc_final: 0.8637 (t-90) REVERT: G 340 LEU cc_start: 0.9280 (mm) cc_final: 0.9002 (pp) REVERT: D 99 ASN cc_start: 0.8335 (p0) cc_final: 0.7779 (p0) REVERT: A 95 MET cc_start: 0.8482 (tpp) cc_final: 0.8234 (tpp) REVERT: A 602 ILE cc_start: 0.8916 (pt) cc_final: 0.8649 (tp) REVERT: A 789 GLU cc_start: 0.8624 (mp0) cc_final: 0.8248 (mp0) REVERT: A 966 TRP cc_start: 0.8415 (m100) cc_final: 0.8160 (m100) REVERT: S 729 LEU cc_start: 0.9141 (mt) cc_final: 0.8879 (mt) REVERT: C 599 GLU cc_start: 0.8401 (mp0) cc_final: 0.8091 (mp0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3454 time to fit residues: 148.3691 Evaluate side-chains 199 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 312 optimal weight: 0.0020 chunk 164 optimal weight: 0.0170 chunk 77 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 320 optimal weight: 0.1980 chunk 226 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 394 optimal weight: 0.7980 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064241 restraints weight = 161072.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065694 restraints weight = 92494.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066690 restraints weight = 62745.510| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30593 Z= 0.098 Angle : 0.497 8.506 43054 Z= 0.253 Chirality : 0.039 0.309 5213 Planarity : 0.004 0.059 4992 Dihedral : 17.171 179.751 7376 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3936 helix: 1.99 (0.13), residues: 1735 sheet: -1.41 (0.26), residues: 389 loop : -0.57 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 749 HIS 0.013 0.001 HIS B 79 PHE 0.015 0.001 PHE A 207 TYR 0.020 0.001 TYR A1091 ARG 0.008 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1503) hydrogen bonds : angle 4.15290 ( 4235) covalent geometry : bond 0.00204 (30593) covalent geometry : angle 0.49748 (43054) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9278 (mm) cc_final: 0.8988 (pp) REVERT: A 95 MET cc_start: 0.8492 (tpp) cc_final: 0.8268 (tpp) REVERT: A 789 GLU cc_start: 0.8587 (mp0) cc_final: 0.8018 (mp0) REVERT: A 1292 GLU cc_start: 0.7616 (tp30) cc_final: 0.7326 (tp30) REVERT: S 729 LEU cc_start: 0.9150 (mt) cc_final: 0.8931 (mt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3388 time to fit residues: 143.9647 Evaluate side-chains 205 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 100 optimal weight: 2.9990 chunk 408 optimal weight: 40.0000 chunk 17 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.079827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062203 restraints weight = 164016.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063638 restraints weight = 94811.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064593 restraints weight = 63757.001| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30593 Z= 0.164 Angle : 0.537 8.916 43054 Z= 0.279 Chirality : 0.040 0.340 5213 Planarity : 0.004 0.056 4992 Dihedral : 17.225 176.494 7376 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3936 helix: 1.79 (0.12), residues: 1746 sheet: -1.45 (0.26), residues: 396 loop : -0.67 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1263 HIS 0.008 0.001 HIS A 755 PHE 0.020 0.002 PHE A 681 TYR 0.025 0.002 TYR A1044 ARG 0.008 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 1503) hydrogen bonds : angle 4.35638 ( 4235) covalent geometry : bond 0.00343 (30593) covalent geometry : angle 0.53739 (43054) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9306 (mm) cc_final: 0.8993 (pp) REVERT: A 95 MET cc_start: 0.8546 (tpp) cc_final: 0.8306 (tpp) REVERT: A 600 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7462 (ptt180) REVERT: A 789 GLU cc_start: 0.8620 (mp0) cc_final: 0.8134 (mp0) REVERT: A 902 TYR cc_start: 0.8048 (m-80) cc_final: 0.7752 (m-80) REVERT: A 1292 GLU cc_start: 0.7612 (tp30) cc_final: 0.7310 (tp30) REVERT: S 729 LEU cc_start: 0.9231 (mt) cc_final: 0.8969 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3543 time to fit residues: 140.9018 Evaluate side-chains 191 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 40.0000 chunk 273 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 374 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 348 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.080244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.062795 restraints weight = 166860.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064127 restraints weight = 98307.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.065027 restraints weight = 67739.433| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30593 Z= 0.151 Angle : 0.527 8.854 43054 Z= 0.273 Chirality : 0.040 0.344 5213 Planarity : 0.004 0.056 4992 Dihedral : 17.246 176.600 7376 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3936 helix: 1.79 (0.13), residues: 1739 sheet: -1.49 (0.25), residues: 411 loop : -0.69 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A1263 HIS 0.017 0.001 HIS G 248 PHE 0.019 0.001 PHE A 681 TYR 0.019 0.001 TYR A1091 ARG 0.010 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 1503) hydrogen bonds : angle 4.34344 ( 4235) covalent geometry : bond 0.00316 (30593) covalent geometry : angle 0.52700 (43054) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 294 HIS cc_start: 0.8786 (t-90) cc_final: 0.8552 (t-90) REVERT: G 340 LEU cc_start: 0.9323 (mm) cc_final: 0.9006 (pp) REVERT: A 95 MET cc_start: 0.8546 (tpp) cc_final: 0.8323 (tpp) REVERT: A 598 LEU cc_start: 0.8885 (mm) cc_final: 0.8658 (mm) REVERT: A 600 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7374 (ptt180) REVERT: A 602 ILE cc_start: 0.8994 (tp) cc_final: 0.8658 (pt) REVERT: A 789 GLU cc_start: 0.8638 (mp0) cc_final: 0.8200 (mp0) REVERT: A 902 TYR cc_start: 0.7974 (m-80) cc_final: 0.7656 (m-80) REVERT: S 729 LEU cc_start: 0.9267 (mt) cc_final: 0.9023 (mt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3565 time to fit residues: 140.5083 Evaluate side-chains 197 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 26 optimal weight: 6.9990 chunk 281 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 244 optimal weight: 30.0000 chunk 168 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062168 restraints weight = 169029.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063491 restraints weight = 99230.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064407 restraints weight = 68396.927| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30593 Z= 0.176 Angle : 0.554 9.270 43054 Z= 0.287 Chirality : 0.041 0.363 5213 Planarity : 0.004 0.058 4992 Dihedral : 17.304 175.642 7376 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3936 helix: 1.67 (0.13), residues: 1739 sheet: -1.53 (0.25), residues: 401 loop : -0.77 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A1263 HIS 0.010 0.001 HIS G 248 PHE 0.021 0.002 PHE A 681 TYR 0.021 0.002 TYR A1091 ARG 0.009 0.001 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1503) hydrogen bonds : angle 4.49393 ( 4235) covalent geometry : bond 0.00370 (30593) covalent geometry : angle 0.55398 (43054) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 307 ILE cc_start: 0.8746 (mm) cc_final: 0.8491 (mm) REVERT: G 340 LEU cc_start: 0.9330 (mm) cc_final: 0.9011 (pp) REVERT: A 95 MET cc_start: 0.8555 (tpp) cc_final: 0.8274 (tpp) REVERT: A 602 ILE cc_start: 0.8994 (tp) cc_final: 0.8791 (mm) REVERT: A 651 TRP cc_start: 0.7711 (t60) cc_final: 0.7460 (t60) REVERT: A 789 GLU cc_start: 0.8514 (mp0) cc_final: 0.8063 (mp0) REVERT: A 902 TYR cc_start: 0.8031 (m-80) cc_final: 0.7728 (m-80) REVERT: S 729 LEU cc_start: 0.9262 (mt) cc_final: 0.9010 (mt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3677 time to fit residues: 140.5615 Evaluate side-chains 193 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 402 optimal weight: 3.9990 chunk 198 optimal weight: 0.0470 chunk 150 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 249 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 410 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063885 restraints weight = 162635.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065342 restraints weight = 93849.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066348 restraints weight = 63316.363| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30593 Z= 0.096 Angle : 0.504 8.658 43054 Z= 0.256 Chirality : 0.039 0.315 5213 Planarity : 0.004 0.054 4992 Dihedral : 17.206 179.470 7376 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3936 helix: 2.03 (0.13), residues: 1733 sheet: -1.49 (0.25), residues: 404 loop : -0.60 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A1263 HIS 0.019 0.001 HIS G 248 PHE 0.013 0.001 PHE A 681 TYR 0.023 0.001 TYR A 783 ARG 0.007 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1503) hydrogen bonds : angle 4.11151 ( 4235) covalent geometry : bond 0.00203 (30593) covalent geometry : angle 0.50444 (43054) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9313.69 seconds wall clock time: 163 minutes 22.65 seconds (9802.65 seconds total)