Starting phenix.real_space_refine on Mon Aug 25 16:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpk_18555/08_2025/8qpk_18555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpk_18555/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qpk_18555/08_2025/8qpk_18555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpk_18555/08_2025/8qpk_18555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qpk_18555/08_2025/8qpk_18555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpk_18555/08_2025/8qpk_18555.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 8, 'GLU:plan': 12, 'ARG:plan': 9, 'ASN:plan1': 1, 'TYR:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1} 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: {'TYR:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 8, 'PHE: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: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 8, 'TYR:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1} 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, 'GLU:plan': 92, 'ASP:plan': 88, 'ARG:plan': 57, 'HIS:plan': 19, 'ASN:plan1': 55, 'PHE:plan': 33, 'TYR:plan': 24, 'TRP:plan': 12} 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: {'GLU:plan': 4, 'ASP:plan': 10, 'TRP:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 1} 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: {'ARG:plan': 18, 'HIS:plan': 16, 'TYR:plan': 23, 'ASP:plan': 23, 'ASN:plan1': 27, 'PHE:plan': 26, 'GLU:plan': 25, 'GLN:plan1': 20, 'TRP:plan': 4} 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: {'GLU:plan': 6, 'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 3, '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: {'ASP:plan': 51, 'PHE:plan': 8, 'ASN:plan1': 14, 'GLU:plan': 49, 'ARG:plan': 16, 'GLN:plan1': 18, 'HIS:plan': 5, 'TYR:plan': 5, 'TRP:plan': 3} 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: {'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 1} 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: {'TYR:plan': 1, 'ASP:plan': 10, 'GLU:plan': 13, 'ARG:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 1} 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: {'GLU:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 1} 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: {'GLU:plan': 5, 'ASP:plan': 1, 'PHE: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: 7.88, per 1000 atoms: 0.27 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.43 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: 11.84 Time building geometry restraints manager: 3.92 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: 11.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 39.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (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 ARG 0.007 0.000 ARG B 51 TYR 0.026 0.001 TYR A1044 PHE 0.019 0.001 PHE A 230 TRP 0.044 0.001 TRP A1263 HIS 0.016 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00228 (30593) covalent geometry : angle 0.49359 (43054) hydrogen bonds : bond 0.17807 ( 1503) hydrogen bonds : angle 6.22551 ( 4235) *********************** 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 : 1.065 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: 0.1520 time to fit residues: 62.1822 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 30.0000 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 328 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.078711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061133 restraints weight = 165287.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062480 restraints weight = 96549.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063415 restraints weight = 66130.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064045 restraints weight = 50582.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064494 restraints weight = 41988.415| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30593 Z= 0.263 Angle : 0.636 17.647 43054 Z= 0.329 Chirality : 0.043 0.456 5213 Planarity : 0.005 0.062 4992 Dihedral : 17.292 175.465 7376 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3936 helix: 1.58 (0.12), residues: 1750 sheet: -1.53 (0.25), residues: 403 loop : -0.62 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 158 TYR 0.021 0.002 TYR A1091 PHE 0.020 0.002 PHE A 387 TRP 0.024 0.002 TRP A 966 HIS 0.016 0.002 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00531 (30593) covalent geometry : angle 0.63612 (43054) hydrogen bonds : bond 0.05593 ( 1503) hydrogen bonds : angle 5.04728 ( 4235) *********************** 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 221 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9311 (mm) cc_final: 0.9014 (pp) REVERT: A 789 GLU cc_start: 0.8708 (mp0) cc_final: 0.8214 (mp0) REVERT: A 902 TYR cc_start: 0.8177 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1292 GLU cc_start: 0.7626 (tp30) cc_final: 0.7150 (tp30) REVERT: S 729 LEU cc_start: 0.9272 (mt) cc_final: 0.9029 (mt) outliers start: 2 outliers final: 1 residues processed: 221 average time/residue: 0.1478 time to fit residues: 56.0912 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 : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 382 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.080273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062689 restraints weight = 167299.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064074 restraints weight = 97784.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065009 restraints weight = 67113.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065695 restraints weight = 51494.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066159 restraints weight = 42668.319| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30593 Z= 0.150 Angle : 0.523 8.659 43054 Z= 0.271 Chirality : 0.040 0.411 5213 Planarity : 0.004 0.058 4992 Dihedral : 17.260 176.777 7376 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3936 helix: 1.75 (0.12), residues: 1739 sheet: -1.55 (0.26), residues: 381 loop : -0.60 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 565 TYR 0.023 0.002 TYR A1044 PHE 0.018 0.001 PHE A 681 TRP 0.024 0.002 TRP A 939 HIS 0.007 0.001 HIS C 642 Details of bonding type rmsd covalent geometry : bond 0.00309 (30593) covalent geometry : angle 0.52277 (43054) hydrogen bonds : bond 0.04626 ( 1503) hydrogen bonds : angle 4.63791 ( 4235) *********************** 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 233 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9337 (mm) cc_final: 0.8981 (pp) REVERT: A 600 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7340 (ptm160) REVERT: A 637 TRP cc_start: 0.8251 (m100) cc_final: 0.8026 (m100) REVERT: A 697 MET cc_start: 0.8336 (tmm) cc_final: 0.8123 (tmm) REVERT: A 789 GLU cc_start: 0.8661 (mp0) cc_final: 0.8215 (mp0) REVERT: A 1292 GLU cc_start: 0.7672 (tp30) cc_final: 0.7265 (tp30) REVERT: S 729 LEU cc_start: 0.9265 (mt) cc_final: 0.8987 (mt) REVERT: S 733 PHE cc_start: 0.8302 (m-10) cc_final: 0.8057 (m-10) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1465 time to fit residues: 58.7091 Evaluate side-chains 194 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 368 optimal weight: 9.9990 chunk 408 optimal weight: 30.0000 chunk 44 optimal weight: 0.7980 chunk 218 optimal weight: 0.5980 chunk 294 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 360 optimal weight: 0.1980 chunk 273 optimal weight: 20.0000 chunk 24 optimal weight: 0.0470 chunk 114 optimal weight: 0.0870 chunk 283 optimal weight: 8.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 837 GLN N 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064311 restraints weight = 161007.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065784 restraints weight = 92004.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.066796 restraints weight = 61995.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067519 restraints weight = 46780.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068034 restraints weight = 38326.483| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30593 Z= 0.097 Angle : 0.488 8.523 43054 Z= 0.249 Chirality : 0.039 0.371 5213 Planarity : 0.004 0.052 4992 Dihedral : 17.099 179.964 7376 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.14), residues: 3936 helix: 2.05 (0.12), residues: 1743 sheet: -1.31 (0.25), residues: 397 loop : -0.50 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 565 TYR 0.020 0.001 TYR A1091 PHE 0.024 0.001 PHE A 207 TRP 0.027 0.002 TRP C 709 HIS 0.012 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00201 (30593) covalent geometry : angle 0.48751 (43054) hydrogen bonds : bond 0.03908 ( 1503) hydrogen bonds : angle 4.17719 ( 4235) *********************** 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 252 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9328 (mm) cc_final: 0.8959 (pp) REVERT: D 4 MET cc_start: 0.8740 (ptp) cc_final: 0.8221 (pmm) REVERT: D 99 ASN cc_start: 0.8219 (p0) cc_final: 0.7833 (p0) REVERT: A 95 MET cc_start: 0.8672 (tpp) cc_final: 0.8294 (tpp) REVERT: A 600 ARG cc_start: 0.7945 (ptm160) cc_final: 0.7436 (ptm160) REVERT: A 602 ILE cc_start: 0.8999 (pt) cc_final: 0.8772 (pt) REVERT: A 789 GLU cc_start: 0.8676 (mp0) cc_final: 0.8389 (mp0) REVERT: A 966 TRP cc_start: 0.8279 (m100) cc_final: 0.8077 (m100) REVERT: A 1031 ILE cc_start: 0.9001 (mm) cc_final: 0.8410 (mm) REVERT: A 1292 GLU cc_start: 0.7738 (tp30) cc_final: 0.7456 (tp30) REVERT: R 413 ILE cc_start: 0.7635 (pt) cc_final: 0.7429 (pt) REVERT: S 729 LEU cc_start: 0.9240 (mt) cc_final: 0.8947 (mt) REVERT: C 245 HIS cc_start: 0.8384 (t70) cc_final: 0.8179 (t70) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.1585 time to fit residues: 68.8346 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 : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 218 optimal weight: 0.0050 chunk 195 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 182 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 351 optimal weight: 0.9980 chunk 226 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 260 optimal weight: 0.2980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 561 HIS A 601 GLN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.082717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064723 restraints weight = 162388.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066188 restraints weight = 92602.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067223 restraints weight = 62632.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067898 restraints weight = 47205.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068436 restraints weight = 38652.785| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1660 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= 0.090 Angle : 0.474 8.626 43054 Z= 0.241 Chirality : 0.039 0.337 5213 Planarity : 0.004 0.049 4992 Dihedral : 17.017 179.540 7376 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3936 helix: 2.11 (0.12), residues: 1754 sheet: -1.15 (0.26), residues: 398 loop : -0.49 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 593 TYR 0.019 0.001 TYR A1091 PHE 0.014 0.001 PHE A 207 TRP 0.020 0.001 TRP A1263 HIS 0.010 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00187 (30593) covalent geometry : angle 0.47390 (43054) hydrogen bonds : bond 0.03744 ( 1503) hydrogen bonds : angle 4.02847 ( 4235) *********************** 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 250 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9291 (mm) cc_final: 0.8970 (pp) REVERT: D 4 MET cc_start: 0.8681 (ptp) cc_final: 0.8285 (pmm) REVERT: A 95 MET cc_start: 0.8775 (tpp) cc_final: 0.8370 (tpp) REVERT: A 600 ARG cc_start: 0.7882 (ptm160) cc_final: 0.7399 (ptt180) REVERT: A 789 GLU cc_start: 0.8631 (mp0) cc_final: 0.8256 (mp0) REVERT: A 1031 ILE cc_start: 0.9030 (mm) cc_final: 0.8490 (mm) REVERT: A 1292 GLU cc_start: 0.7755 (tp30) cc_final: 0.7457 (tp30) REVERT: R 413 ILE cc_start: 0.7750 (pt) cc_final: 0.7532 (pt) REVERT: S 729 LEU cc_start: 0.9239 (mt) cc_final: 0.8954 (mt) REVERT: B 57 GLN cc_start: 0.6793 (pp30) cc_final: 0.6358 (pp30) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1762 time to fit residues: 74.8873 Evaluate side-chains 206 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 140 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 400 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 561 HIS A 601 GLN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.081318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063634 restraints weight = 162078.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065051 restraints weight = 93732.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066010 restraints weight = 63765.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.066695 restraints weight = 48640.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067097 restraints weight = 40160.966| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30593 Z= 0.136 Angle : 0.500 11.681 43054 Z= 0.256 Chirality : 0.040 0.369 5213 Planarity : 0.004 0.051 4992 Dihedral : 17.039 178.645 7376 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3936 helix: 2.11 (0.13), residues: 1757 sheet: -1.19 (0.26), residues: 389 loop : -0.48 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 593 TYR 0.024 0.001 TYR A1044 PHE 0.016 0.001 PHE A 681 TRP 0.040 0.001 TRP A 651 HIS 0.014 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00286 (30593) covalent geometry : angle 0.50018 (43054) hydrogen bonds : bond 0.03825 ( 1503) hydrogen bonds : angle 4.10069 ( 4235) *********************** 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 237 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9301 (mm) cc_final: 0.8953 (pp) REVERT: D 4 MET cc_start: 0.8642 (ptp) cc_final: 0.8157 (pmm) REVERT: A 95 MET cc_start: 0.8710 (tpp) cc_final: 0.8317 (tpp) REVERT: A 789 GLU cc_start: 0.8530 (mp0) cc_final: 0.8101 (mp0) REVERT: S 729 LEU cc_start: 0.9226 (mt) cc_final: 0.8914 (mt) REVERT: B 57 GLN cc_start: 0.6892 (pp30) cc_final: 0.6334 (pp30) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1660 time to fit residues: 67.8581 Evaluate side-chains 195 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 331 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 361 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 561 HIS A 601 GLN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064027 restraints weight = 161585.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065471 restraints weight = 92989.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.066483 restraints weight = 62976.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067190 restraints weight = 47602.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067614 restraints weight = 39071.600| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1821 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= 0.102 Angle : 0.486 8.858 43054 Z= 0.246 Chirality : 0.039 0.353 5213 Planarity : 0.004 0.050 4992 Dihedral : 17.017 178.998 7376 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.14), residues: 3936 helix: 2.16 (0.12), residues: 1757 sheet: -1.14 (0.26), residues: 382 loop : -0.47 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 593 TYR 0.019 0.001 TYR A1091 PHE 0.014 0.001 PHE A 681 TRP 0.020 0.001 TRP A1263 HIS 0.008 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00214 (30593) covalent geometry : angle 0.48580 (43054) hydrogen bonds : bond 0.03679 ( 1503) hydrogen bonds : angle 3.99637 ( 4235) *********************** 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 245 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9294 (mm) cc_final: 0.8935 (pp) REVERT: D 4 MET cc_start: 0.8573 (ptp) cc_final: 0.8113 (pmm) REVERT: A 95 MET cc_start: 0.8757 (tpp) cc_final: 0.8351 (tpp) REVERT: A 602 ILE cc_start: 0.8975 (tp) cc_final: 0.8656 (pt) REVERT: A 789 GLU cc_start: 0.8576 (mp0) cc_final: 0.8255 (mp0) REVERT: A 1031 ILE cc_start: 0.9098 (mm) cc_final: 0.8575 (mm) REVERT: R 413 ILE cc_start: 0.7804 (pt) cc_final: 0.7575 (pt) REVERT: S 729 LEU cc_start: 0.9214 (mt) cc_final: 0.8933 (mt) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1680 time to fit residues: 71.0653 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 : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 206 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 246 optimal weight: 20.0000 chunk 342 optimal weight: 7.9990 chunk 164 optimal weight: 0.0370 chunk 133 optimal weight: 0.7980 chunk 404 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 318 optimal weight: 0.8980 chunk 144 optimal weight: 0.0370 overall best weight: 1.1538 ------------------------------------------------------------------------------- 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 561 HIS ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 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 = 0.3693 r_free = 0.3693 target = 0.081594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063857 restraints weight = 161331.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065284 restraints weight = 93211.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066278 restraints weight = 63183.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066979 restraints weight = 47843.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067337 restraints weight = 39256.046| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1900 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= 0.111 Angle : 0.491 8.895 43054 Z= 0.249 Chirality : 0.039 0.356 5213 Planarity : 0.004 0.060 4992 Dihedral : 17.006 178.677 7376 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.14), residues: 3936 helix: 2.17 (0.12), residues: 1757 sheet: -1.09 (0.26), residues: 391 loop : -0.49 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 593 TYR 0.019 0.001 TYR A1091 PHE 0.017 0.001 PHE A 640 TRP 0.048 0.001 TRP A 651 HIS 0.015 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00236 (30593) covalent geometry : angle 0.49050 (43054) hydrogen bonds : bond 0.03647 ( 1503) hydrogen bonds : angle 3.98449 ( 4235) *********************** 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 237 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9318 (mm) cc_final: 0.8949 (pp) REVERT: D 4 MET cc_start: 0.8569 (ptp) cc_final: 0.8038 (pmm) REVERT: A 95 MET cc_start: 0.8721 (tpp) cc_final: 0.8265 (tpp) REVERT: A 600 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7395 (ptt180) REVERT: A 789 GLU cc_start: 0.8666 (mp0) cc_final: 0.8286 (mp0) REVERT: A 1031 ILE cc_start: 0.9040 (mm) cc_final: 0.8501 (mm) REVERT: S 729 LEU cc_start: 0.9242 (mt) cc_final: 0.8991 (mt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1712 time to fit residues: 69.6431 Evaluate side-chains 200 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 367 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 394 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 268 optimal weight: 30.0000 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 561 HIS ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 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 = 0.3659 r_free = 0.3659 target = 0.080151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062491 restraints weight = 162395.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063892 restraints weight = 94442.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064861 restraints weight = 64015.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065484 restraints weight = 48890.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065967 restraints weight = 40463.701| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30593 Z= 0.172 Angle : 0.544 9.085 43054 Z= 0.281 Chirality : 0.040 0.384 5213 Planarity : 0.004 0.057 4992 Dihedral : 17.122 176.291 7376 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3936 helix: 1.94 (0.12), residues: 1757 sheet: -1.23 (0.26), residues: 396 loop : -0.60 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 565 TYR 0.020 0.002 TYR A1091 PHE 0.020 0.002 PHE A 681 TRP 0.062 0.002 TRP A 651 HIS 0.009 0.001 HIS A 545 Details of bonding type rmsd covalent geometry : bond 0.00359 (30593) covalent geometry : angle 0.54432 (43054) hydrogen bonds : bond 0.04022 ( 1503) hydrogen bonds : angle 4.26099 ( 4235) *********************** 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 230 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: G 294 HIS cc_start: 0.8746 (t-90) cc_final: 0.8518 (t-90) REVERT: G 340 LEU cc_start: 0.9333 (mm) cc_final: 0.8960 (pp) REVERT: A 95 MET cc_start: 0.8631 (tpp) cc_final: 0.8160 (tpp) REVERT: A 789 GLU cc_start: 0.8620 (mp0) cc_final: 0.8207 (mp0) REVERT: A 902 TYR cc_start: 0.8048 (m-80) cc_final: 0.7745 (m-80) REVERT: S 729 LEU cc_start: 0.9264 (mt) cc_final: 0.9028 (mt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1663 time to fit residues: 66.2588 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 269 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 234 optimal weight: 0.0050 chunk 325 optimal weight: 1.9990 chunk 311 optimal weight: 0.3980 chunk 289 optimal weight: 0.0060 chunk 46 optimal weight: 2.9990 chunk 217 optimal weight: 30.0000 chunk 83 optimal weight: 0.7980 chunk 383 optimal weight: 6.9990 chunk 375 optimal weight: 20.0000 overall best weight: 0.4210 ------------------------------------------------------------------------------- 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 994 ASN ** S 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 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 = 0.3706 r_free = 0.3706 target = 0.082489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064876 restraints weight = 165092.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066249 restraints weight = 96500.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.067256 restraints weight = 66553.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067928 restraints weight = 50723.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068397 restraints weight = 41904.457| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2028 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= 0.094 Angle : 0.504 11.462 43054 Z= 0.253 Chirality : 0.039 0.334 5213 Planarity : 0.004 0.061 4992 Dihedral : 17.048 178.836 7376 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 3936 helix: 2.13 (0.12), residues: 1755 sheet: -1.28 (0.25), residues: 415 loop : -0.46 (0.16), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 565 TYR 0.025 0.001 TYR D 46 PHE 0.018 0.001 PHE C 883 TRP 0.062 0.002 TRP A1263 HIS 0.015 0.001 HIS G 248 Details of bonding type rmsd covalent geometry : bond 0.00200 (30593) covalent geometry : angle 0.50404 (43054) hydrogen bonds : bond 0.03619 ( 1503) hydrogen bonds : angle 4.00403 ( 4235) ********************** 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 238 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 340 LEU cc_start: 0.9300 (mm) cc_final: 0.8937 (pp) REVERT: A 95 MET cc_start: 0.8714 (tpp) cc_final: 0.8273 (tpp) REVERT: A 600 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7253 (ptt180) REVERT: A 789 GLU cc_start: 0.8607 (mp0) cc_final: 0.8236 (mp0) REVERT: R 413 ILE cc_start: 0.7768 (pt) cc_final: 0.7537 (pt) REVERT: S 729 LEU cc_start: 0.9187 (mt) cc_final: 0.8930 (mt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1400 time to fit residues: 57.0731 Evaluate side-chains 202 residues out of total 3568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 311 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** 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** ** B 57 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 = 0.3699 r_free = 0.3699 target = 0.081922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064185 restraints weight = 160701.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065616 restraints weight = 92886.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066598 restraints weight = 63120.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.067300 restraints weight = 47752.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.067699 restraints weight = 39450.748| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2090 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= 0.101 Angle : 0.495 9.786 43054 Z= 0.250 Chirality : 0.039 0.335 5213 Planarity : 0.004 0.056 4992 Dihedral : 17.003 179.110 7376 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 3936 helix: 2.16 (0.12), residues: 1761 sheet: -1.23 (0.25), residues: 418 loop : -0.44 (0.16), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1136 TYR 0.022 0.001 TYR D 46 PHE 0.015 0.001 PHE A 640 TRP 0.038 0.001 TRP A1263 HIS 0.007 0.001 HIS A 755 Details of bonding type rmsd covalent geometry : bond 0.00216 (30593) covalent geometry : angle 0.49494 (43054) hydrogen bonds : bond 0.03527 ( 1503) hydrogen bonds : angle 3.96374 ( 4235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.93 seconds wall clock time: 90 minutes 25.26 seconds (5425.26 seconds total)