Starting phenix.real_space_refine on Mon Jul 6 01:38:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pec_13352/07_2026/7pec_13352.map" } resolution = 4.24 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= 0.013 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 6 5.49 5 S 203 5.16 5 C 19672 2.51 5 N 5414 2.21 5 O 5616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30911 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1856 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 15598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1949, 15598 Classifications: {'peptide': 1949} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 80, 'TRANS': 1868} Chain breaks: 12 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'UNK:plan-1': 25, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "I" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2580 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 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: 6.20, per 1000 atoms: 0.20 Number of scatterers: 30911 At special positions: 0 Unit cell: (250.2, 167.912, 151.232, 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 203 16.00 P 6 15.00 O 5616 8.00 N 5414 7.00 C 19672 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: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7396 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 25 sheets defined 64.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.966A pdb=" N UNK A 24 " --> pdb=" O UNK A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.640A pdb=" N UNK A 52 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.858A pdb=" N LEU A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.323A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.872A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.755A pdb=" N VAL A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.605A pdb=" N LEU A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.827A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.775A pdb=" N UNK A 371 " --> pdb=" O UNK A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 380 through 380 No H-bonds generated for 'chain 'A' and resid 380 through 380' Processing helix chain 'A' and resid 387 through 403 removed outlier: 3.669A pdb=" N THR A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Proline residue: A 397 - end of helix removed outlier: 3.501A pdb=" N PHE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.766A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.893A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 451 through 463 removed outlier: 3.802A pdb=" N ILE A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.557A pdb=" N PHE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.109A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.691A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 549 removed outlier: 3.741A pdb=" N HIS A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.457A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 4.037A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.728A pdb=" N ARG A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 666 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.633A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 Processing helix chain 'A' and resid 722 through 744 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.556A pdb=" N ILE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.842A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 829 removed outlier: 4.471A pdb=" N ASP A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 852 Processing helix chain 'A' and resid 855 through 861 removed outlier: 3.705A pdb=" N ARG A 859 " --> pdb=" O VAL A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.910A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 891 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 942 through 960 Proline residue: A 948 - end of helix removed outlier: 3.871A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 967 removed outlier: 4.030A pdb=" N HIS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 962 through 967' Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.673A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.654A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 4.225A pdb=" N GLU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1042 removed outlier: 4.537A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 removed outlier: 3.555A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 3.836A pdb=" N LYS A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1084 removed outlier: 3.858A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.753A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 removed outlier: 3.538A pdb=" N ASP A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A1109 " --> pdb=" O ASN A1106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1105 through 1109' Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1146 removed outlier: 3.726A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1166 removed outlier: 3.552A pdb=" N ILE A1155 " --> pdb=" O TYR A1151 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.640A pdb=" N ASP A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 4.028A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1202 removed outlier: 3.579A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1262 through 1270 removed outlier: 3.724A pdb=" N GLN A1266 " --> pdb=" O THR A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1295 removed outlier: 3.538A pdb=" N TRP A1280 " --> pdb=" O SER A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 3.682A pdb=" N ALA A1314 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 3.549A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1391 removed outlier: 3.668A pdb=" N GLY A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1441 removed outlier: 3.576A pdb=" N ALA A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.028A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 4.469A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1536 removed outlier: 3.504A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1556 through 1581 removed outlier: 3.506A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1608 removed outlier: 3.888A pdb=" N ALA A1586 " --> pdb=" O SER A1582 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A1604 " --> pdb=" O GLU A1600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1626 removed outlier: 3.603A pdb=" N GLY A1625 " --> pdb=" O GLU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1641 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1663 removed outlier: 4.084A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1693 through 1707 removed outlier: 3.578A pdb=" N LYS A1706 " --> pdb=" O LYS A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1732 Processing helix chain 'A' and resid 1737 through 1762 Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 3.757A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1812 removed outlier: 3.683A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1896 removed outlier: 3.564A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.528A pdb=" N SER A1895 " --> pdb=" O SER A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 Processing helix chain 'A' and resid 1933 through 1937 Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.794A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1967 removed outlier: 3.582A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1971 Processing helix chain 'A' and resid 1972 through 1981 removed outlier: 3.518A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2002 removed outlier: 3.573A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A2002 " --> pdb=" O MET A1998 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2021 Processing helix chain 'A' and resid 2022 through 2039 Processing helix chain 'A' and resid 2043 through 2059 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2092 removed outlier: 3.704A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.747A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.849A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 Processing helix chain 'A' and resid 2212 through 2219 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2293 Processing helix chain 'A' and resid 2297 through 2307 Processing helix chain 'A' and resid 2309 through 2335 Processing helix chain 'A' and resid 2363 through 2368 Processing helix chain 'A' and resid 2380 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2424 removed outlier: 3.688A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP A2424 " --> pdb=" O ALA A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2427 through 2435 removed outlier: 4.512A pdb=" N LEU A2431 " --> pdb=" O LEU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2493 through 2510 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2541 removed outlier: 3.747A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS A2541 " --> pdb=" O ASN A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.914A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E 94 " --> pdb=" O PRO E 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 94' Processing helix chain 'E' and resid 94 through 114 removed outlier: 4.073A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 removed outlier: 3.559A pdb=" N MET E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 219 removed outlier: 4.104A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 285 removed outlier: 6.320A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.788A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.714A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 422 removed outlier: 3.936A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'E' and resid 445 through 459 removed outlier: 3.656A pdb=" N LEU E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.579A pdb=" N VAL E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.561A pdb=" N LYS E 478 " --> pdb=" O PRO E 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 479 " --> pdb=" O TYR E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 484 through 486 No H-bonds generated for 'chain 'E' and resid 484 through 486' Processing helix chain 'E' and resid 487 through 502 removed outlier: 3.582A pdb=" N VAL E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.511A pdb=" N VAL E 510 " --> pdb=" O GLN E 506 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 511 " --> pdb=" O ALA E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 523 removed outlier: 3.579A pdb=" N PHE E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 521 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 removed outlier: 3.548A pdb=" N GLN E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.835A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 629 removed outlier: 3.753A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 649 removed outlier: 3.787A pdb=" N THR E 638 " --> pdb=" O THR E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 674 removed outlier: 3.521A pdb=" N GLU E 662 " --> pdb=" O MET E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.604A pdb=" N THR E 680 " --> pdb=" O SER E 676 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 removed outlier: 3.590A pdb=" N HIS E 817 " --> pdb=" O ARG E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.596A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 removed outlier: 3.576A pdb=" N ALA E 953 " --> pdb=" O PHE E 950 " (cutoff:3.500A) Processing helix chain 'E' and resid 958 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 982 through 1008 Processing helix chain 'I' and resid 21 through 48 removed outlier: 3.804A pdb=" N ARG I 29 " --> pdb=" O ARG I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 77 removed outlier: 3.647A pdb=" N ILE I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 96 Processing helix chain 'I' and resid 127 through 145 Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 182 through 197 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.679A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 removed outlier: 3.623A pdb=" N ASP A2244 " --> pdb=" O LEU A2346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.335A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.836A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 88 through 91 removed outlier: 3.761A pdb=" N ARG C 110 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLY C 104 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 123 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 131 through 136 removed outlier: 4.192A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.161A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 228 removed outlier: 6.662A pdb=" N CYS C 238 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS C 226 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 236 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE C 228 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 234 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 258 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 277 through 278 removed outlier: 3.546A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 118 through 123 removed outlier: 3.585A pdb=" N LEU E 62 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 59 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N HIS E 149 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA E 61 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN E 151 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL E 63 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AB4, first strand: chain 'E' and resid 1015 through 1021 removed outlier: 3.789A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL E1327 " --> pdb=" O ILE E1017 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU E1019 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E1325 " --> pdb=" O LEU E1019 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1029 through 1031 removed outlier: 3.559A pdb=" N LYS E1030 " --> pdb=" O ALA E1039 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E1039 " --> pdb=" O LYS E1030 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE E1046 " --> pdb=" O TYR E1059 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR E1059 " --> pdb=" O ILE E1046 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE E1048 " --> pdb=" O LEU E1057 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1070 through 1076 removed outlier: 3.783A pdb=" N ALA E1072 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E1087 " --> pdb=" O ALA E1072 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA E1092 " --> pdb=" O THR E1088 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1127 through 1128 Processing sheet with id=AB8, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.587A pdb=" N GLU E1132 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E1137 " --> pdb=" O GLU E1132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 1146 through 1151 removed outlier: 3.753A pdb=" N GLN E1159 " --> pdb=" O ILE E1149 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP E1151 " --> pdb=" O LYS E1157 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E1157 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 1181 through 1184 removed outlier: 6.873A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1227 through 1230 removed outlier: 3.762A pdb=" N SER E1229 " --> pdb=" O ARG E1237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1267 through 1269 removed outlier: 3.766A pdb=" N ASN E1288 " --> pdb=" O ILE E1279 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 51 through 55 removed outlier: 5.425A pdb=" N LYS I 51 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN I 62 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N ASN I 62 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N PHE I 117 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE I 64 " --> pdb=" O TYR I 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 152 through 156 removed outlier: 6.379A pdb=" N ARG I 154 " --> pdb=" O GLU I 162 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU I 162 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU I 156 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG I 163 " --> pdb=" O PHE I 217 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE I 217 " --> pdb=" O ARG I 163 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE I 165 " --> pdb=" O TYR I 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 329 through 333 removed outlier: 4.749A pdb=" N SER I 374 " --> pdb=" O GLU I 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.529A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) 1714 hydrogen bonds defined for protein. 5019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.67 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10196 1.34 - 1.46: 6721 1.46 - 1.58: 14316 1.58 - 1.69: 6 1.69 - 1.81: 327 Bond restraints: 31566 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.599 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.617 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.442 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O16 IHP A2601 " pdb=" P6 IHP A2601 " ideal model delta sigma weight residual 1.672 1.620 0.052 2.00e-02 2.50e+03 6.82e+00 ... (remaining 31561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 42226 1.63 - 3.27: 451 3.27 - 4.90: 99 4.90 - 6.53: 25 6.53 - 8.17: 5 Bond angle restraints: 42806 Sorted by residual: angle pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " ideal model delta sigma weight residual 112.00 119.62 -7.62 2.20e+00 2.07e-01 1.20e+01 angle pdb=" C GLU A 429 " pdb=" N ARG A 430 " pdb=" CA ARG A 430 " ideal model delta sigma weight residual 120.38 124.94 -4.56 1.46e+00 4.69e-01 9.77e+00 angle pdb=" CA PRO I 325 " pdb=" N PRO I 325 " pdb=" CD PRO I 325 " ideal model delta sigma weight residual 112.00 108.36 3.64 1.40e+00 5.10e-01 6.77e+00 angle pdb=" C4 IHP A2601 " pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 120.75 128.53 -7.78 3.00e+00 1.11e-01 6.72e+00 angle pdb=" C GLY I 323 " pdb=" N ALA I 324 " pdb=" CA ALA I 324 " ideal model delta sigma weight residual 121.80 128.12 -6.32 2.44e+00 1.68e-01 6.71e+00 ... (remaining 42801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 17139 17.25 - 34.50: 1432 34.50 - 51.75: 379 51.75 - 69.01: 99 69.01 - 86.26: 20 Dihedral angle restraints: 19069 sinusoidal: 7721 harmonic: 11348 Sorted by residual: dihedral pdb=" CA ALA I 324 " pdb=" C ALA I 324 " pdb=" N PRO I 325 " pdb=" CA PRO I 325 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE E1060 " pdb=" C PHE E1060 " pdb=" N HIS E1061 " pdb=" CA HIS E1061 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sinusoidal sigma weight residual -90.00 -26.73 -63.27 2 1.50e+01 4.44e-03 1.70e+01 ... (remaining 19066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4109 0.054 - 0.107: 653 0.107 - 0.161: 80 0.161 - 0.215: 2 0.215 - 0.268: 2 Chirality restraints: 4846 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.58 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O15 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.42 -2.59 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4843 not shown) Planarity restraints: 5459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E1105 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO E1106 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E1106 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E1106 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 324 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO I 325 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO I 325 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 325 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A1158 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.029 5.00e-02 4.00e+02 ... (remaining 5456 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5385 2.77 - 3.30: 30864 3.30 - 3.84: 51017 3.84 - 4.37: 60171 4.37 - 4.90: 100860 Nonbonded interactions: 248297 Sorted by model distance: nonbonded pdb=" O GLY A2337 " pdb=" NH1 ARG A2339 " model vdw 2.238 3.120 nonbonded pdb=" O GLN I 152 " pdb=" OG1 THR I 164 " model vdw 2.253 3.040 nonbonded pdb=" O THR E1163 " pdb=" OH TYR E1193 " model vdw 2.266 3.040 nonbonded pdb=" NH1 ARG A2018 " pdb=" OE2 GLU A2067 " model vdw 2.270 3.120 nonbonded pdb=" OG SER A1658 " pdb=" O32 IHP A2601 " model vdw 2.275 3.040 ... (remaining 248292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.080 31566 Z= 0.106 Angle : 0.485 8.167 42806 Z= 0.252 Chirality : 0.039 0.268 4846 Planarity : 0.004 0.057 5459 Dihedral : 14.496 86.257 11673 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 4.99 % Allowed : 6.72 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3768 helix: -0.78 (0.10), residues: 2150 sheet: -3.17 (0.22), residues: 375 loop : -1.23 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 882 TYR 0.015 0.001 TYR E 475 PHE 0.017 0.001 PHE A 610 TRP 0.013 0.001 TRP A 199 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (31566) covalent geometry : angle 0.48537 / 0.25 (42806) hydrogen bonds : bond 0.24290 / 15.85 ( 1714) hydrogen bonds : angle 7.46547 / 5.19 ( 5019) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 671 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.7426 (mmm) cc_final: 0.7192 (tpp) REVERT: A 733 MET cc_start: 0.9486 (mmm) cc_final: 0.9105 (mmm) REVERT: A 772 MET cc_start: 0.8653 (tmm) cc_final: 0.8342 (tmm) REVERT: A 808 VAL cc_start: 0.9428 (t) cc_final: 0.8597 (p) REVERT: A 822 ILE cc_start: 0.9657 (mt) cc_final: 0.9055 (tp) REVERT: A 824 ILE cc_start: 0.9669 (mt) cc_final: 0.9434 (tp) REVERT: A 828 LEU cc_start: 0.9361 (mt) cc_final: 0.8754 (mt) REVERT: A 851 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8092 (t) REVERT: A 863 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8858 (p) REVERT: A 994 MET cc_start: 0.9104 (tpp) cc_final: 0.8622 (tpp) REVERT: A 1031 MET cc_start: 0.9147 (tpp) cc_final: 0.8696 (tpp) REVERT: A 1055 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9175 (tm) REVERT: A 1074 LEU cc_start: 0.9709 (mt) cc_final: 0.9464 (mp) REVERT: A 1146 LEU cc_start: 0.9156 (mt) cc_final: 0.8589 (mt) REVERT: A 1183 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9145 (tt0) REVERT: A 1317 LEU cc_start: 0.9466 (mt) cc_final: 0.9248 (mt) REVERT: A 1470 ASN cc_start: 0.8675 (m-40) cc_final: 0.8453 (t0) REVERT: A 1477 MET cc_start: 0.9265 (ttp) cc_final: 0.9019 (tpt) REVERT: A 1601 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 1632 ASP cc_start: 0.8786 (m-30) cc_final: 0.8165 (m-30) REVERT: A 1634 GLN cc_start: 0.9163 (tt0) cc_final: 0.8780 (tm-30) REVERT: A 1650 MET cc_start: 0.8077 (mmt) cc_final: 0.7595 (mmm) REVERT: A 1701 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: A 1752 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9270 (tt) REVERT: A 1900 LEU cc_start: 0.9444 (tp) cc_final: 0.8968 (tt) REVERT: A 1988 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8395 (p-80) REVERT: A 2014 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8818 (tm-30) REVERT: A 2026 MET cc_start: 0.9397 (mtp) cc_final: 0.8829 (ttm) REVERT: A 2029 GLU cc_start: 0.9057 (pt0) cc_final: 0.8722 (pp20) REVERT: A 2234 SER cc_start: 0.9538 (p) cc_final: 0.9263 (t) REVERT: A 2260 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9172 (tt) REVERT: A 2329 MET cc_start: 0.9301 (mmp) cc_final: 0.9073 (mmm) REVERT: A 2357 ASP cc_start: 0.8201 (t0) cc_final: 0.7730 (t0) REVERT: A 2389 VAL cc_start: 0.9167 (m) cc_final: 0.8457 (m) REVERT: A 2412 ASP cc_start: 0.9121 (m-30) cc_final: 0.8746 (p0) REVERT: A 2415 MET cc_start: 0.9216 (mmm) cc_final: 0.8731 (tpp) REVERT: C 143 LEU cc_start: 0.9563 (tp) cc_final: 0.9336 (tt) REVERT: C 228 PHE cc_start: 0.7100 (m-80) cc_final: 0.6875 (m-10) REVERT: C 243 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8493 (p) REVERT: C 255 MET cc_start: 0.8628 (ttp) cc_final: 0.8192 (tmm) REVERT: E 36 CYS cc_start: 0.9048 (m) cc_final: 0.8797 (p) REVERT: E 93 MET cc_start: 0.8513 (mtp) cc_final: 0.8163 (mtm) REVERT: E 192 PHE cc_start: 0.8596 (m-80) cc_final: 0.8175 (m-80) REVERT: E 328 LEU cc_start: 0.9511 (mt) cc_final: 0.9269 (mp) REVERT: E 351 LEU cc_start: 0.9472 (mt) cc_final: 0.9096 (mt) REVERT: E 354 GLU cc_start: 0.9243 (tt0) cc_final: 0.8862 (tm-30) REVERT: E 383 ASP cc_start: 0.9186 (m-30) cc_final: 0.8981 (t0) REVERT: E 567 ASN cc_start: 0.9018 (m-40) cc_final: 0.8512 (t0) REVERT: E 625 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7396 (p) REVERT: E 828 ASP cc_start: 0.9425 (m-30) cc_final: 0.9181 (m-30) REVERT: E 984 ILE cc_start: 0.9748 (mt) cc_final: 0.9467 (pt) REVERT: E 1050 ASP cc_start: 0.7379 (t0) cc_final: 0.6951 (t70) REVERT: E 1060 PHE cc_start: 0.5478 (m-10) cc_final: 0.5038 (m-10) REVERT: E 1163 THR cc_start: 0.7396 (m) cc_final: 0.7098 (p) REVERT: E 1285 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8614 (tm-30) REVERT: I 130 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8578 (p) REVERT: I 155 GLU cc_start: 0.8872 (tt0) cc_final: 0.8540 (tm-30) REVERT: I 189 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7847 (mp) REVERT: I 199 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8568 (tp) REVERT: I 200 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: I 210 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6593 (t0) outliers start: 167 outliers final: 24 residues processed: 802 average time/residue: 0.2129 time to fit residues: 268.8386 Evaluate side-chains 402 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 363 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 85 ASN C 87 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN I 99 HIS ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.083526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062529 restraints weight = 175260.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.064174 restraints weight = 95047.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.065219 restraints weight = 63123.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.065927 restraints weight = 45919.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.066443 restraints weight = 36806.002| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31566 Z= 0.168 Angle : 0.654 11.639 42806 Z= 0.340 Chirality : 0.043 0.194 4846 Planarity : 0.005 0.059 5459 Dihedral : 4.499 50.218 4199 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 0.15 % Allowed : 2.36 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3768 helix: 0.93 (0.10), residues: 2200 sheet: -2.84 (0.23), residues: 375 loop : -0.96 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A2378 TYR 0.031 0.002 TYR E1324 PHE 0.025 0.002 PHE A1122 TRP 0.030 0.002 TRP C 112 HIS 0.016 0.001 HIS A1988 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (31566) covalent geometry : angle 0.65446 / 0.34 (42806) hydrogen bonds : bond 0.05587 / 3.67 ( 1714) hydrogen bonds : angle 5.01631 / 3.47 ( 5019) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 453 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9374 (mmm) cc_final: 0.8948 (mmm) REVERT: A 772 MET cc_start: 0.8743 (tmm) cc_final: 0.8465 (tmm) REVERT: A 822 ILE cc_start: 0.9668 (mt) cc_final: 0.9268 (tp) REVERT: A 824 ILE cc_start: 0.9725 (mt) cc_final: 0.9467 (tp) REVERT: A 827 MET cc_start: 0.9013 (tmm) cc_final: 0.8748 (tmm) REVERT: A 828 LEU cc_start: 0.9337 (mt) cc_final: 0.8894 (mt) REVERT: A 956 MET cc_start: 0.9303 (tpp) cc_final: 0.8710 (tpp) REVERT: A 994 MET cc_start: 0.9061 (tpp) cc_final: 0.8540 (tpp) REVERT: A 1031 MET cc_start: 0.9197 (tpp) cc_final: 0.8743 (tpp) REVERT: A 1033 GLU cc_start: 0.9139 (mp0) cc_final: 0.8856 (mp0) REVERT: A 1035 VAL cc_start: 0.9675 (p) cc_final: 0.9454 (p) REVERT: A 1146 LEU cc_start: 0.8965 (mt) cc_final: 0.8636 (mt) REVERT: A 1477 MET cc_start: 0.9300 (ttp) cc_final: 0.8902 (tpp) REVERT: A 1481 MET cc_start: 0.8810 (mtm) cc_final: 0.8517 (ptp) REVERT: A 1596 LEU cc_start: 0.9696 (mt) cc_final: 0.9462 (mt) REVERT: A 1598 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 1601 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 1632 ASP cc_start: 0.8832 (m-30) cc_final: 0.8611 (m-30) REVERT: A 1650 MET cc_start: 0.8250 (mmt) cc_final: 0.7887 (mmm) REVERT: A 1743 LEU cc_start: 0.9094 (tt) cc_final: 0.8680 (tp) REVERT: A 1747 MET cc_start: 0.8723 (ttm) cc_final: 0.8171 (ttm) REVERT: A 1753 LYS cc_start: 0.9566 (mmtt) cc_final: 0.9283 (mmmm) REVERT: A 1760 ASN cc_start: 0.9314 (m-40) cc_final: 0.9060 (t0) REVERT: A 1900 LEU cc_start: 0.9440 (tp) cc_final: 0.9216 (tt) REVERT: A 1930 ILE cc_start: 0.9029 (tt) cc_final: 0.8812 (tt) REVERT: A 1964 ILE cc_start: 0.9485 (mm) cc_final: 0.8971 (tp) REVERT: A 2026 MET cc_start: 0.9438 (mtp) cc_final: 0.9105 (mtp) REVERT: A 2029 GLU cc_start: 0.9089 (pt0) cc_final: 0.8792 (pp20) REVERT: A 2327 MET cc_start: 0.8831 (tpt) cc_final: 0.8530 (tpt) REVERT: A 2329 MET cc_start: 0.9417 (mmp) cc_final: 0.9167 (mmm) REVERT: A 2382 MET cc_start: 0.8732 (mmm) cc_final: 0.8488 (mmt) REVERT: A 2412 ASP cc_start: 0.9069 (m-30) cc_final: 0.8712 (p0) REVERT: A 2526 GLU cc_start: 0.9260 (tp30) cc_final: 0.8866 (tp30) REVERT: C 143 LEU cc_start: 0.9434 (tp) cc_final: 0.9163 (tt) REVERT: C 255 MET cc_start: 0.8710 (ttp) cc_final: 0.8472 (tmm) REVERT: C 273 MET cc_start: 0.8443 (ttp) cc_final: 0.7072 (ppp) REVERT: C 293 LEU cc_start: 0.8769 (mt) cc_final: 0.8442 (mm) REVERT: E 51 MET cc_start: 0.8317 (tpp) cc_final: 0.8078 (tpp) REVERT: E 71 ASP cc_start: 0.9134 (p0) cc_final: 0.8880 (p0) REVERT: E 186 MET cc_start: 0.8530 (mmm) cc_final: 0.8201 (mmm) REVERT: E 192 PHE cc_start: 0.8822 (m-80) cc_final: 0.8220 (m-80) REVERT: E 328 LEU cc_start: 0.9522 (mt) cc_final: 0.9243 (mp) REVERT: E 351 LEU cc_start: 0.9400 (mt) cc_final: 0.8970 (mt) REVERT: E 534 MET cc_start: 0.8512 (mtt) cc_final: 0.8282 (mtt) REVERT: E 567 ASN cc_start: 0.9057 (m-40) cc_final: 0.8614 (t0) REVERT: E 625 THR cc_start: 0.7629 (m) cc_final: 0.7346 (p) REVERT: E 961 ASP cc_start: 0.8830 (t70) cc_final: 0.8452 (t0) REVERT: E 1055 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7968 (pm20) REVERT: E 1150 TRP cc_start: 0.6407 (m100) cc_final: 0.6138 (m100) REVERT: E 1205 MET cc_start: 0.6748 (mtt) cc_final: 0.5697 (ttm) REVERT: E 1285 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8608 (tm-30) REVERT: I 144 MET cc_start: 0.7422 (mtt) cc_final: 0.7076 (mtt) REVERT: I 194 MET cc_start: 0.9524 (tpp) cc_final: 0.9121 (tpt) REVERT: I 369 CYS cc_start: 0.8466 (m) cc_final: 0.8195 (m) outliers start: 5 outliers final: 0 residues processed: 456 average time/residue: 0.2018 time to fit residues: 148.1602 Evaluate side-chains 320 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 343 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 361 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS A 262 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN E 198 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 601 HIS ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.081801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061064 restraints weight = 176913.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.062691 restraints weight = 96154.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.063844 restraints weight = 64670.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064577 restraints weight = 46947.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065012 restraints weight = 37626.917| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31566 Z= 0.167 Angle : 0.611 9.737 42806 Z= 0.315 Chirality : 0.041 0.215 4846 Planarity : 0.005 0.060 5459 Dihedral : 4.430 51.955 4199 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3768 helix: 1.28 (0.11), residues: 2212 sheet: -2.50 (0.23), residues: 379 loop : -0.94 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1094 TYR 0.030 0.002 TYR E1324 PHE 0.022 0.002 PHE A1122 TRP 0.066 0.002 TRP A1269 HIS 0.009 0.001 HIS A2401 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (31566) covalent geometry : angle 0.61081 / 0.31 (42806) hydrogen bonds : bond 0.04821 / 3.16 ( 1714) hydrogen bonds : angle 4.76100 / 3.29 ( 5019) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9402 (mmm) cc_final: 0.8965 (mmp) REVERT: A 822 ILE cc_start: 0.9686 (mt) cc_final: 0.9291 (tp) REVERT: A 824 ILE cc_start: 0.9740 (mt) cc_final: 0.9472 (tp) REVERT: A 828 LEU cc_start: 0.9353 (mt) cc_final: 0.8966 (mt) REVERT: A 956 MET cc_start: 0.9389 (tpp) cc_final: 0.8841 (tpp) REVERT: A 994 MET cc_start: 0.9176 (tpp) cc_final: 0.8655 (tpp) REVERT: A 1031 MET cc_start: 0.9221 (tpp) cc_final: 0.8766 (tpp) REVERT: A 1033 GLU cc_start: 0.9241 (mp0) cc_final: 0.8915 (mp0) REVERT: A 1074 LEU cc_start: 0.9751 (mp) cc_final: 0.9534 (mp) REVERT: A 1146 LEU cc_start: 0.8974 (mt) cc_final: 0.8677 (mt) REVERT: A 1199 LEU cc_start: 0.9389 (mt) cc_final: 0.9021 (mt) REVERT: A 1313 MET cc_start: 0.8411 (mmp) cc_final: 0.8147 (mmt) REVERT: A 1316 ASP cc_start: 0.8861 (t0) cc_final: 0.8636 (t0) REVERT: A 1364 MET cc_start: 0.9175 (mmm) cc_final: 0.8661 (mmm) REVERT: A 1467 MET cc_start: 0.9004 (mtp) cc_final: 0.8544 (mtp) REVERT: A 1477 MET cc_start: 0.9330 (ttp) cc_final: 0.8965 (tpp) REVERT: A 1481 MET cc_start: 0.8869 (mtm) cc_final: 0.8596 (ptp) REVERT: A 1598 GLU cc_start: 0.8762 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 1601 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8475 (mt-10) REVERT: A 1632 ASP cc_start: 0.8826 (m-30) cc_final: 0.8611 (m-30) REVERT: A 1634 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 1638 MET cc_start: 0.8257 (mmp) cc_final: 0.7942 (mmp) REVERT: A 1650 MET cc_start: 0.8085 (mmt) cc_final: 0.7745 (mmm) REVERT: A 1747 MET cc_start: 0.8935 (ttm) cc_final: 0.8570 (ttm) REVERT: A 1761 LEU cc_start: 0.9159 (mt) cc_final: 0.8952 (mt) REVERT: A 1804 TYR cc_start: 0.7771 (m-80) cc_final: 0.7491 (m-10) REVERT: A 1964 ILE cc_start: 0.9469 (mm) cc_final: 0.8869 (tp) REVERT: A 2026 MET cc_start: 0.9468 (mtp) cc_final: 0.9083 (mtt) REVERT: A 2029 GLU cc_start: 0.9145 (pt0) cc_final: 0.8824 (pp20) REVERT: A 2199 MET cc_start: 0.8750 (tpp) cc_final: 0.8470 (tpp) REVERT: A 2271 MET cc_start: 0.9141 (tpp) cc_final: 0.8931 (tpp) REVERT: A 2303 LEU cc_start: 0.9600 (mt) cc_final: 0.9387 (mt) REVERT: A 2327 MET cc_start: 0.8932 (tpt) cc_final: 0.8598 (tpt) REVERT: A 2382 MET cc_start: 0.8878 (mmm) cc_final: 0.8599 (mmt) REVERT: A 2412 ASP cc_start: 0.9047 (m-30) cc_final: 0.8762 (p0) REVERT: A 2415 MET cc_start: 0.9125 (tpp) cc_final: 0.8753 (tpp) REVERT: A 2506 ASP cc_start: 0.8763 (t0) cc_final: 0.8551 (t0) REVERT: A 2526 GLU cc_start: 0.9381 (tp30) cc_final: 0.8858 (tp30) REVERT: C 100 MET cc_start: 0.8541 (ppp) cc_final: 0.8038 (ppp) REVERT: C 273 MET cc_start: 0.8135 (ttp) cc_final: 0.7059 (ppp) REVERT: C 293 LEU cc_start: 0.8747 (mt) cc_final: 0.8439 (mm) REVERT: E 51 MET cc_start: 0.8445 (tpp) cc_final: 0.7905 (tpp) REVERT: E 71 ASP cc_start: 0.9158 (p0) cc_final: 0.8883 (p0) REVERT: E 97 LYS cc_start: 0.9320 (tptp) cc_final: 0.9071 (tppt) REVERT: E 186 MET cc_start: 0.8467 (mmm) cc_final: 0.8215 (mmm) REVERT: E 192 PHE cc_start: 0.8883 (m-80) cc_final: 0.8212 (m-80) REVERT: E 207 LYS cc_start: 0.9837 (mtmt) cc_final: 0.9622 (mttp) REVERT: E 254 MET cc_start: 0.8924 (tpp) cc_final: 0.8578 (tpp) REVERT: E 328 LEU cc_start: 0.9552 (mt) cc_final: 0.9278 (mp) REVERT: E 567 ASN cc_start: 0.9018 (m-40) cc_final: 0.8637 (t0) REVERT: E 615 VAL cc_start: 0.9107 (t) cc_final: 0.8752 (p) REVERT: E 625 THR cc_start: 0.7342 (m) cc_final: 0.7071 (p) REVERT: E 659 VAL cc_start: 0.8283 (t) cc_final: 0.8073 (t) REVERT: E 961 ASP cc_start: 0.8854 (t70) cc_final: 0.8469 (t0) REVERT: E 967 PHE cc_start: 0.7729 (m-10) cc_final: 0.7507 (m-10) REVERT: E 1055 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7961 (pm20) REVERT: E 1108 MET cc_start: 0.8699 (tpt) cc_final: 0.7887 (tpt) REVERT: E 1150 TRP cc_start: 0.6567 (m100) cc_final: 0.6344 (m100) REVERT: E 1197 MET cc_start: 0.7432 (ptt) cc_final: 0.7139 (ptt) REVERT: E 1205 MET cc_start: 0.6957 (mtt) cc_final: 0.5928 (ttm) REVERT: E 1285 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8633 (tm-30) REVERT: E 1324 TYR cc_start: 0.7137 (m-80) cc_final: 0.6892 (m-80) REVERT: I 144 MET cc_start: 0.7457 (mtt) cc_final: 0.7045 (mtt) REVERT: I 194 MET cc_start: 0.9527 (tpp) cc_final: 0.9088 (tpt) REVERT: I 355 VAL cc_start: 0.8594 (t) cc_final: 0.8293 (t) REVERT: I 366 MET cc_start: 0.7223 (mpp) cc_final: 0.6952 (mpp) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1996 time to fit residues: 124.8670 Evaluate side-chains 287 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 285 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 282 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.081377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060793 restraints weight = 178443.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062276 restraints weight = 102077.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063379 restraints weight = 67517.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.064154 restraints weight = 49393.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064529 restraints weight = 39920.138| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31566 Z= 0.158 Angle : 0.594 11.987 42806 Z= 0.303 Chirality : 0.041 0.230 4846 Planarity : 0.004 0.064 5459 Dihedral : 4.379 52.491 4199 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3768 helix: 1.44 (0.11), residues: 2208 sheet: -2.23 (0.24), residues: 371 loop : -0.84 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 154 TYR 0.023 0.002 TYR A2332 PHE 0.038 0.002 PHE A1103 TRP 0.061 0.001 TRP A1269 HIS 0.007 0.001 HIS A2355 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (31566) covalent geometry : angle 0.59424 / 0.30 (42806) hydrogen bonds : bond 0.04311 / 2.82 ( 1714) hydrogen bonds : angle 4.58825 / 3.15 ( 5019) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9387 (mmm) cc_final: 0.8934 (mmp) REVERT: A 813 MET cc_start: 0.8519 (ppp) cc_final: 0.7504 (ppp) REVERT: A 956 MET cc_start: 0.9411 (tpp) cc_final: 0.8887 (tpp) REVERT: A 994 MET cc_start: 0.9227 (tpp) cc_final: 0.8691 (tpp) REVERT: A 1031 MET cc_start: 0.9243 (tpp) cc_final: 0.8835 (tpp) REVERT: A 1032 ASP cc_start: 0.9303 (p0) cc_final: 0.8938 (p0) REVERT: A 1033 GLU cc_start: 0.9272 (mp0) cc_final: 0.8857 (mp0) REVERT: A 1058 GLN cc_start: 0.9287 (mp10) cc_final: 0.8608 (mt0) REVERT: A 1071 LEU cc_start: 0.9576 (tp) cc_final: 0.9322 (tp) REVERT: A 1074 LEU cc_start: 0.9706 (mp) cc_final: 0.9469 (mp) REVERT: A 1078 MET cc_start: 0.9324 (pmm) cc_final: 0.9054 (pmm) REVERT: A 1146 LEU cc_start: 0.8996 (mt) cc_final: 0.8684 (mt) REVERT: A 1199 LEU cc_start: 0.9163 (mt) cc_final: 0.8946 (mt) REVERT: A 1313 MET cc_start: 0.8385 (mmp) cc_final: 0.7552 (mmp) REVERT: A 1316 ASP cc_start: 0.9115 (t0) cc_final: 0.8876 (p0) REVERT: A 1317 LEU cc_start: 0.9625 (mt) cc_final: 0.9360 (mt) REVERT: A 1364 MET cc_start: 0.9252 (mmm) cc_final: 0.8643 (mmm) REVERT: A 1477 MET cc_start: 0.9428 (ttp) cc_final: 0.9114 (tpt) REVERT: A 1481 MET cc_start: 0.8969 (mtm) cc_final: 0.8495 (ptp) REVERT: A 1515 MET cc_start: 0.9415 (mmp) cc_final: 0.9207 (mmm) REVERT: A 1578 MET cc_start: 0.8536 (tpt) cc_final: 0.8108 (tpp) REVERT: A 1598 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 1601 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 1634 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 1650 MET cc_start: 0.8099 (mmt) cc_final: 0.7780 (mmm) REVERT: A 1761 LEU cc_start: 0.9240 (mt) cc_final: 0.8955 (mt) REVERT: A 1804 TYR cc_start: 0.7748 (m-80) cc_final: 0.7478 (m-10) REVERT: A 2026 MET cc_start: 0.9474 (mtp) cc_final: 0.9086 (mtt) REVERT: A 2029 GLU cc_start: 0.9209 (pt0) cc_final: 0.8912 (pp20) REVERT: A 2199 MET cc_start: 0.8847 (tpp) cc_final: 0.8534 (tpp) REVERT: A 2268 MET cc_start: 0.9161 (mmm) cc_final: 0.8489 (mmm) REVERT: A 2303 LEU cc_start: 0.9593 (mt) cc_final: 0.9355 (mt) REVERT: A 2346 LEU cc_start: 0.9367 (tt) cc_final: 0.9142 (tt) REVERT: A 2357 ASP cc_start: 0.8190 (t0) cc_final: 0.7905 (t0) REVERT: A 2382 MET cc_start: 0.8933 (mmm) cc_final: 0.8701 (mmt) REVERT: A 2412 ASP cc_start: 0.9064 (m-30) cc_final: 0.8792 (p0) REVERT: A 2526 GLU cc_start: 0.9425 (tp30) cc_final: 0.8924 (tp30) REVERT: C 67 MET cc_start: 0.8564 (mtp) cc_final: 0.8343 (mtp) REVERT: C 100 MET cc_start: 0.8533 (ppp) cc_final: 0.7979 (ppp) REVERT: C 227 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8413 (mmm-85) REVERT: C 273 MET cc_start: 0.8010 (ttp) cc_final: 0.7265 (ppp) REVERT: C 293 LEU cc_start: 0.8715 (mt) cc_final: 0.8429 (mm) REVERT: E 51 MET cc_start: 0.8407 (tpp) cc_final: 0.7834 (tpp) REVERT: E 55 MET cc_start: 0.6081 (mmm) cc_final: 0.5852 (mmm) REVERT: E 71 ASP cc_start: 0.9221 (p0) cc_final: 0.8971 (p0) REVERT: E 93 MET cc_start: 0.8248 (ptp) cc_final: 0.7860 (ptt) REVERT: E 97 LYS cc_start: 0.9180 (tptp) cc_final: 0.8831 (tppt) REVERT: E 186 MET cc_start: 0.8527 (mmm) cc_final: 0.8283 (mmm) REVERT: E 192 PHE cc_start: 0.8854 (m-80) cc_final: 0.8145 (m-80) REVERT: E 207 LYS cc_start: 0.9846 (mtmt) cc_final: 0.9587 (mtmm) REVERT: E 254 MET cc_start: 0.9034 (tpp) cc_final: 0.8646 (tpp) REVERT: E 328 LEU cc_start: 0.9539 (mt) cc_final: 0.9251 (mp) REVERT: E 567 ASN cc_start: 0.9048 (m-40) cc_final: 0.8688 (t0) REVERT: E 615 VAL cc_start: 0.9071 (t) cc_final: 0.8739 (p) REVERT: E 625 THR cc_start: 0.7233 (m) cc_final: 0.6984 (p) REVERT: E 961 ASP cc_start: 0.8853 (t70) cc_final: 0.8581 (t0) REVERT: E 972 MET cc_start: 0.7396 (ptp) cc_final: 0.7188 (ttm) REVERT: E 1055 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8051 (pm20) REVERT: E 1108 MET cc_start: 0.8685 (tpt) cc_final: 0.7984 (tpt) REVERT: E 1150 TRP cc_start: 0.6617 (m100) cc_final: 0.6128 (m100) REVERT: E 1197 MET cc_start: 0.7468 (ptt) cc_final: 0.7212 (ptt) REVERT: E 1205 MET cc_start: 0.6865 (mtt) cc_final: 0.5838 (ttp) REVERT: E 1285 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8636 (tm-30) REVERT: I 144 MET cc_start: 0.7377 (mtt) cc_final: 0.7010 (mtt) REVERT: I 194 MET cc_start: 0.9547 (tpp) cc_final: 0.9119 (tpt) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1963 time to fit residues: 117.9331 Evaluate side-chains 275 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 145 optimal weight: 0.7980 chunk 308 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 378 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS I 188 GLN ** I 191 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.081887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061421 restraints weight = 176155.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063079 restraints weight = 97590.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.063946 restraints weight = 64384.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.064746 restraints weight = 48881.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.065057 restraints weight = 39530.772| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31566 Z= 0.125 Angle : 0.566 7.399 42806 Z= 0.288 Chirality : 0.041 0.229 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.326 52.736 4199 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3768 helix: 1.54 (0.11), residues: 2211 sheet: -2.00 (0.25), residues: 369 loop : -0.84 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1021 TYR 0.019 0.001 TYR E 605 PHE 0.037 0.001 PHE A 434 TRP 0.066 0.001 TRP A1269 HIS 0.006 0.001 HIS A2401 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31566) covalent geometry : angle 0.56589 / 0.29 (42806) hydrogen bonds : bond 0.03994 / 2.62 ( 1714) hydrogen bonds : angle 4.41804 / 3.04 ( 5019) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9361 (mmm) cc_final: 0.8911 (mmp) REVERT: A 813 MET cc_start: 0.8545 (ppp) cc_final: 0.7630 (ppp) REVERT: A 956 MET cc_start: 0.9396 (tpp) cc_final: 0.8882 (tpp) REVERT: A 994 MET cc_start: 0.9254 (tpp) cc_final: 0.8675 (tpp) REVERT: A 1031 MET cc_start: 0.9236 (tpp) cc_final: 0.8801 (tpp) REVERT: A 1032 ASP cc_start: 0.9321 (p0) cc_final: 0.9022 (p0) REVERT: A 1033 GLU cc_start: 0.9203 (mp0) cc_final: 0.8839 (mp0) REVERT: A 1078 MET cc_start: 0.9354 (pmm) cc_final: 0.9044 (pmm) REVERT: A 1146 LEU cc_start: 0.8977 (mt) cc_final: 0.8690 (mt) REVERT: A 1313 MET cc_start: 0.8269 (mmp) cc_final: 0.7410 (mmp) REVERT: A 1317 LEU cc_start: 0.9624 (mt) cc_final: 0.9394 (mt) REVERT: A 1364 MET cc_start: 0.9255 (mmm) cc_final: 0.8435 (mmm) REVERT: A 1467 MET cc_start: 0.8940 (mtp) cc_final: 0.8567 (mtp) REVERT: A 1477 MET cc_start: 0.9392 (ttp) cc_final: 0.9017 (tpp) REVERT: A 1481 MET cc_start: 0.8804 (mtm) cc_final: 0.8574 (ptp) REVERT: A 1598 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 1601 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 1632 ASP cc_start: 0.8923 (m-30) cc_final: 0.8706 (m-30) REVERT: A 1634 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8878 (tm-30) REVERT: A 1650 MET cc_start: 0.8054 (mmt) cc_final: 0.7796 (mmm) REVERT: A 1747 MET cc_start: 0.8845 (ttm) cc_final: 0.8014 (ttm) REVERT: A 1761 LEU cc_start: 0.9216 (mt) cc_final: 0.8900 (mt) REVERT: A 1804 TYR cc_start: 0.7711 (m-80) cc_final: 0.7482 (m-10) REVERT: A 1879 MET cc_start: 0.8963 (ptp) cc_final: 0.8760 (ptp) REVERT: A 2026 MET cc_start: 0.9470 (mtp) cc_final: 0.9075 (mtt) REVERT: A 2029 GLU cc_start: 0.9194 (pt0) cc_final: 0.8904 (pp20) REVERT: A 2199 MET cc_start: 0.8862 (tpp) cc_final: 0.8560 (tpp) REVERT: A 2268 MET cc_start: 0.9101 (mmm) cc_final: 0.8518 (mmm) REVERT: A 2303 LEU cc_start: 0.9591 (mt) cc_final: 0.9384 (mt) REVERT: A 2346 LEU cc_start: 0.9304 (tt) cc_final: 0.9086 (tt) REVERT: A 2357 ASP cc_start: 0.8160 (t0) cc_final: 0.7867 (t0) REVERT: A 2366 MET cc_start: 0.8736 (mmt) cc_final: 0.8463 (mmm) REVERT: A 2382 MET cc_start: 0.8979 (mmm) cc_final: 0.8754 (mmt) REVERT: A 2412 ASP cc_start: 0.9040 (m-30) cc_final: 0.8792 (p0) REVERT: A 2506 ASP cc_start: 0.8853 (t0) cc_final: 0.8653 (t0) REVERT: A 2526 GLU cc_start: 0.9449 (tp30) cc_final: 0.8922 (tp30) REVERT: C 67 MET cc_start: 0.8546 (mtp) cc_final: 0.8325 (mtp) REVERT: C 100 MET cc_start: 0.8429 (ppp) cc_final: 0.7881 (ppp) REVERT: C 227 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8552 (mmm-85) REVERT: C 255 MET cc_start: 0.8881 (ttm) cc_final: 0.8392 (tmm) REVERT: C 293 LEU cc_start: 0.8669 (mt) cc_final: 0.8362 (mm) REVERT: E 51 MET cc_start: 0.8413 (tpp) cc_final: 0.7853 (tpp) REVERT: E 55 MET cc_start: 0.6222 (mmm) cc_final: 0.5551 (mmm) REVERT: E 71 ASP cc_start: 0.9188 (p0) cc_final: 0.8954 (p0) REVERT: E 93 MET cc_start: 0.8238 (ptp) cc_final: 0.7911 (ptt) REVERT: E 97 LYS cc_start: 0.9173 (tptp) cc_final: 0.8897 (tppt) REVERT: E 186 MET cc_start: 0.8608 (mmm) cc_final: 0.8355 (mmm) REVERT: E 192 PHE cc_start: 0.8717 (m-80) cc_final: 0.8011 (m-80) REVERT: E 207 LYS cc_start: 0.9840 (mtmt) cc_final: 0.9582 (mtmm) REVERT: E 328 LEU cc_start: 0.9535 (mt) cc_final: 0.9256 (mp) REVERT: E 567 ASN cc_start: 0.8961 (m-40) cc_final: 0.8595 (t0) REVERT: E 615 VAL cc_start: 0.9015 (t) cc_final: 0.8673 (p) REVERT: E 625 THR cc_start: 0.7238 (m) cc_final: 0.7010 (p) REVERT: E 961 ASP cc_start: 0.8795 (t70) cc_final: 0.8471 (t70) REVERT: E 1055 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8072 (pm20) REVERT: E 1108 MET cc_start: 0.8538 (tpt) cc_final: 0.8073 (tpt) REVERT: E 1150 TRP cc_start: 0.6578 (m100) cc_final: 0.6224 (m100) REVERT: E 1205 MET cc_start: 0.6777 (mtt) cc_final: 0.5913 (ttm) REVERT: E 1285 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8602 (tm-30) REVERT: I 144 MET cc_start: 0.7470 (mtt) cc_final: 0.7134 (mtt) REVERT: I 194 MET cc_start: 0.9531 (tpp) cc_final: 0.9128 (tpt) REVERT: I 366 MET cc_start: 0.7388 (mpp) cc_final: 0.6965 (mpp) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1920 time to fit residues: 113.4299 Evaluate side-chains 265 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 269 optimal weight: 0.0970 chunk 370 optimal weight: 8.9990 chunk 237 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 151 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.081901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061278 restraints weight = 177636.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.062779 restraints weight = 96552.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.063861 restraints weight = 62808.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.064565 restraints weight = 46919.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.065069 restraints weight = 37938.535| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31566 Z= 0.118 Angle : 0.565 9.749 42806 Z= 0.284 Chirality : 0.040 0.225 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.253 53.156 4199 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3768 helix: 1.58 (0.11), residues: 2215 sheet: -1.73 (0.25), residues: 383 loop : -0.79 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 616 TYR 0.032 0.001 TYR A2423 PHE 0.022 0.001 PHE A1122 TRP 0.072 0.001 TRP A1269 HIS 0.007 0.001 HIS A2401 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (31566) covalent geometry : angle 0.56476 / 0.28 (42806) hydrogen bonds : bond 0.03778 / 2.47 ( 1714) hydrogen bonds : angle 4.30528 / 2.96 ( 5019) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8252 (tpp80) REVERT: A 733 MET cc_start: 0.9373 (mmm) cc_final: 0.8953 (mmp) REVERT: A 813 MET cc_start: 0.8606 (ppp) cc_final: 0.7759 (ppp) REVERT: A 956 MET cc_start: 0.9387 (tpp) cc_final: 0.8878 (tpp) REVERT: A 994 MET cc_start: 0.9283 (tpp) cc_final: 0.8686 (tpp) REVERT: A 1031 MET cc_start: 0.9269 (tpp) cc_final: 0.8850 (tpp) REVERT: A 1032 ASP cc_start: 0.9300 (p0) cc_final: 0.8990 (p0) REVERT: A 1033 GLU cc_start: 0.9226 (mp0) cc_final: 0.8821 (mp0) REVERT: A 1078 MET cc_start: 0.9325 (pmm) cc_final: 0.9090 (pmm) REVERT: A 1146 LEU cc_start: 0.8979 (mt) cc_final: 0.8743 (mt) REVERT: A 1199 LEU cc_start: 0.9102 (mt) cc_final: 0.8829 (mt) REVERT: A 1364 MET cc_start: 0.9287 (mmm) cc_final: 0.8454 (mmm) REVERT: A 1452 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8821 (pttm) REVERT: A 1481 MET cc_start: 0.8973 (mtm) cc_final: 0.8551 (mtm) REVERT: A 1512 MET cc_start: 0.8795 (ppp) cc_final: 0.8246 (ppp) REVERT: A 1578 MET cc_start: 0.8755 (tpp) cc_final: 0.8431 (tpp) REVERT: A 1598 GLU cc_start: 0.8659 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 1601 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8142 (mt-10) REVERT: A 1632 ASP cc_start: 0.8932 (m-30) cc_final: 0.8673 (m-30) REVERT: A 1634 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8928 (tm-30) REVERT: A 1717 MET cc_start: 0.9177 (tpt) cc_final: 0.8954 (tpt) REVERT: A 1761 LEU cc_start: 0.9239 (mt) cc_final: 0.8940 (mt) REVERT: A 1804 TYR cc_start: 0.7735 (m-80) cc_final: 0.7444 (m-80) REVERT: A 2014 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8818 (tm-30) REVERT: A 2026 MET cc_start: 0.9469 (mtp) cc_final: 0.9060 (mtt) REVERT: A 2029 GLU cc_start: 0.9200 (pt0) cc_final: 0.8910 (pp20) REVERT: A 2199 MET cc_start: 0.8913 (tpp) cc_final: 0.8588 (tpp) REVERT: A 2220 LEU cc_start: 0.9561 (mt) cc_final: 0.9359 (mt) REVERT: A 2303 LEU cc_start: 0.9590 (mt) cc_final: 0.9378 (mt) REVERT: A 2327 MET cc_start: 0.9106 (tpp) cc_final: 0.8336 (tmm) REVERT: A 2357 ASP cc_start: 0.8178 (t0) cc_final: 0.7901 (t0) REVERT: A 2366 MET cc_start: 0.8762 (mmt) cc_final: 0.8486 (mmm) REVERT: A 2382 MET cc_start: 0.8999 (mmm) cc_final: 0.8767 (mmt) REVERT: A 2412 ASP cc_start: 0.9061 (m-30) cc_final: 0.8832 (p0) REVERT: A 2526 GLU cc_start: 0.9474 (tp30) cc_final: 0.8931 (tp30) REVERT: C 67 MET cc_start: 0.8556 (mtp) cc_final: 0.8339 (mtp) REVERT: C 273 MET cc_start: 0.7851 (ttp) cc_final: 0.7161 (ppp) REVERT: C 293 LEU cc_start: 0.8669 (mt) cc_final: 0.8363 (mm) REVERT: E 51 MET cc_start: 0.8447 (tpp) cc_final: 0.7919 (tpp) REVERT: E 55 MET cc_start: 0.6201 (mmm) cc_final: 0.5580 (mmm) REVERT: E 71 ASP cc_start: 0.9182 (p0) cc_final: 0.8937 (p0) REVERT: E 93 MET cc_start: 0.8371 (ptp) cc_final: 0.8053 (ptt) REVERT: E 97 LYS cc_start: 0.9144 (tptp) cc_final: 0.8855 (tppt) REVERT: E 186 MET cc_start: 0.8640 (mmm) cc_final: 0.8381 (mmm) REVERT: E 192 PHE cc_start: 0.8645 (m-80) cc_final: 0.7989 (m-80) REVERT: E 207 LYS cc_start: 0.9840 (mtmt) cc_final: 0.9581 (mtmm) REVERT: E 328 LEU cc_start: 0.9516 (mt) cc_final: 0.9239 (mp) REVERT: E 567 ASN cc_start: 0.8988 (m-40) cc_final: 0.8632 (t0) REVERT: E 615 VAL cc_start: 0.8992 (t) cc_final: 0.8643 (p) REVERT: E 625 THR cc_start: 0.7170 (m) cc_final: 0.6954 (p) REVERT: E 1055 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7979 (pm20) REVERT: E 1108 MET cc_start: 0.8468 (tpt) cc_final: 0.7966 (tpt) REVERT: E 1150 TRP cc_start: 0.6814 (m100) cc_final: 0.6356 (m100) REVERT: E 1205 MET cc_start: 0.6596 (mtt) cc_final: 0.5608 (ptm) REVERT: E 1243 MET cc_start: 0.5436 (ttt) cc_final: 0.5198 (ttt) REVERT: E 1285 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8679 (tm-30) REVERT: I 144 MET cc_start: 0.7484 (mtt) cc_final: 0.7235 (mtt) REVERT: I 194 MET cc_start: 0.9540 (tpp) cc_final: 0.9145 (tpt) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1783 time to fit residues: 103.9182 Evaluate side-chains 264 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 21 optimal weight: 0.0970 chunk 353 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.081893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.061231 restraints weight = 177955.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.062861 restraints weight = 97707.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.063775 restraints weight = 64159.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.064510 restraints weight = 47905.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064961 restraints weight = 38462.322| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31566 Z= 0.120 Angle : 0.567 9.391 42806 Z= 0.285 Chirality : 0.040 0.220 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.225 53.602 4199 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3768 helix: 1.63 (0.11), residues: 2215 sheet: -1.57 (0.25), residues: 380 loop : -0.77 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2060 TYR 0.027 0.001 TYR A2423 PHE 0.022 0.001 PHE A1122 TRP 0.074 0.001 TRP A1269 HIS 0.007 0.001 HIS A2401 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (31566) covalent geometry : angle 0.56657 / 0.29 (42806) hydrogen bonds : bond 0.03670 / 2.40 ( 1714) hydrogen bonds : angle 4.24597 / 2.93 ( 5019) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9349 (mmm) cc_final: 0.8880 (mmp) REVERT: A 813 MET cc_start: 0.8700 (ppp) cc_final: 0.7891 (ppp) REVERT: A 956 MET cc_start: 0.9353 (tpp) cc_final: 0.8873 (tpp) REVERT: A 994 MET cc_start: 0.9299 (tpp) cc_final: 0.8685 (tpp) REVERT: A 1031 MET cc_start: 0.9242 (tpp) cc_final: 0.8672 (tpp) REVERT: A 1033 GLU cc_start: 0.9172 (mp0) cc_final: 0.8893 (mp0) REVERT: A 1078 MET cc_start: 0.9322 (pmm) cc_final: 0.9091 (pmm) REVERT: A 1146 LEU cc_start: 0.8952 (mt) cc_final: 0.8678 (mt) REVERT: A 1313 MET cc_start: 0.8486 (mmp) cc_final: 0.8072 (mmp) REVERT: A 1364 MET cc_start: 0.9283 (mmm) cc_final: 0.8431 (mmm) REVERT: A 1477 MET cc_start: 0.9357 (tpt) cc_final: 0.8701 (tpp) REVERT: A 1481 MET cc_start: 0.8887 (mtm) cc_final: 0.8566 (ptp) REVERT: A 1512 MET cc_start: 0.8891 (ppp) cc_final: 0.8337 (ppp) REVERT: A 1578 MET cc_start: 0.8724 (tpp) cc_final: 0.8342 (tpp) REVERT: A 1598 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 1599 LEU cc_start: 0.9663 (tp) cc_final: 0.9421 (tt) REVERT: A 1601 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 1634 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8945 (tm-30) REVERT: A 1650 MET cc_start: 0.8519 (mmp) cc_final: 0.8304 (mmm) REVERT: A 1747 MET cc_start: 0.8849 (ttt) cc_final: 0.8462 (ttm) REVERT: A 1761 LEU cc_start: 0.9257 (mt) cc_final: 0.8950 (mt) REVERT: A 1804 TYR cc_start: 0.7735 (m-80) cc_final: 0.7476 (m-10) REVERT: A 1964 ILE cc_start: 0.9344 (mm) cc_final: 0.8554 (tp) REVERT: A 2014 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8811 (tm-30) REVERT: A 2026 MET cc_start: 0.9459 (mtp) cc_final: 0.9043 (mtt) REVERT: A 2029 GLU cc_start: 0.9216 (pt0) cc_final: 0.8925 (pp20) REVERT: A 2199 MET cc_start: 0.8955 (tpp) cc_final: 0.8575 (tpp) REVERT: A 2220 LEU cc_start: 0.9553 (mt) cc_final: 0.9340 (mt) REVERT: A 2268 MET cc_start: 0.9102 (tpp) cc_final: 0.8851 (tpp) REVERT: A 2303 LEU cc_start: 0.9589 (mt) cc_final: 0.9372 (mt) REVERT: A 2327 MET cc_start: 0.9057 (tpp) cc_final: 0.8321 (tmm) REVERT: A 2357 ASP cc_start: 0.8136 (t0) cc_final: 0.7869 (t0) REVERT: A 2366 MET cc_start: 0.8750 (mmt) cc_final: 0.8492 (mmm) REVERT: A 2382 MET cc_start: 0.9010 (mmm) cc_final: 0.8779 (mmt) REVERT: A 2412 ASP cc_start: 0.9070 (m-30) cc_final: 0.8831 (p0) REVERT: A 2526 GLU cc_start: 0.9481 (tp30) cc_final: 0.8952 (tp30) REVERT: C 67 MET cc_start: 0.8559 (mtp) cc_final: 0.8344 (mtp) REVERT: C 100 MET cc_start: 0.8430 (ppp) cc_final: 0.7935 (ppp) REVERT: C 293 LEU cc_start: 0.8629 (mt) cc_final: 0.8334 (mm) REVERT: E 55 MET cc_start: 0.6233 (mmm) cc_final: 0.5594 (mmm) REVERT: E 71 ASP cc_start: 0.9178 (p0) cc_final: 0.8914 (p0) REVERT: E 93 MET cc_start: 0.8436 (ptp) cc_final: 0.8038 (ptt) REVERT: E 97 LYS cc_start: 0.9136 (tptp) cc_final: 0.8809 (tppt) REVERT: E 186 MET cc_start: 0.8632 (mmm) cc_final: 0.8418 (mmm) REVERT: E 192 PHE cc_start: 0.8617 (m-80) cc_final: 0.7849 (m-80) REVERT: E 207 LYS cc_start: 0.9836 (mtmt) cc_final: 0.9572 (mtmm) REVERT: E 328 LEU cc_start: 0.9519 (mt) cc_final: 0.9245 (mp) REVERT: E 567 ASN cc_start: 0.8963 (m-40) cc_final: 0.8609 (t0) REVERT: E 615 VAL cc_start: 0.9024 (t) cc_final: 0.8681 (p) REVERT: E 625 THR cc_start: 0.7538 (m) cc_final: 0.7164 (p) REVERT: E 1055 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8033 (pm20) REVERT: E 1105 ASN cc_start: 0.9616 (m-40) cc_final: 0.9197 (p0) REVERT: E 1108 MET cc_start: 0.8486 (tpt) cc_final: 0.8008 (tpt) REVERT: E 1150 TRP cc_start: 0.6656 (m100) cc_final: 0.6206 (m100) REVERT: E 1205 MET cc_start: 0.6531 (mtt) cc_final: 0.5506 (ptm) REVERT: E 1243 MET cc_start: 0.5452 (ttt) cc_final: 0.5166 (ttt) REVERT: E 1285 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8646 (tm-30) REVERT: I 144 MET cc_start: 0.7491 (mtt) cc_final: 0.7236 (mtt) REVERT: I 194 MET cc_start: 0.9522 (tpp) cc_final: 0.9159 (tpt) REVERT: I 366 MET cc_start: 0.7469 (mpp) cc_final: 0.7008 (mpp) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1756 time to fit residues: 99.1952 Evaluate side-chains 266 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 167 optimal weight: 0.0050 chunk 196 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 233 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 51 optimal weight: 0.9980 chunk 264 optimal weight: 8.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1022 ASN ** I 191 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.082125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061363 restraints weight = 178224.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.062834 restraints weight = 99165.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.063826 restraints weight = 64233.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.064678 restraints weight = 47462.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064941 restraints weight = 38313.100| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31566 Z= 0.115 Angle : 0.573 12.215 42806 Z= 0.287 Chirality : 0.040 0.223 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.222 54.019 4199 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % 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 are not related in a simple way. whole: 0.87 (0.14), residues: 3768 helix: 1.68 (0.11), residues: 2212 sheet: -1.56 (0.25), residues: 386 loop : -0.73 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 616 TYR 0.021 0.001 TYR A2423 PHE 0.021 0.001 PHE A1122 TRP 0.079 0.001 TRP A1269 HIS 0.006 0.001 HIS A2401 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (31566) covalent geometry : angle 0.57291 / 0.29 (42806) hydrogen bonds : bond 0.03570 / 2.34 ( 1714) hydrogen bonds : angle 4.20116 / 2.89 ( 5019) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9378 (mmm) cc_final: 0.8961 (mmm) REVERT: A 813 MET cc_start: 0.8737 (ppp) cc_final: 0.8007 (ppp) REVERT: A 826 ASP cc_start: 0.9260 (m-30) cc_final: 0.8807 (p0) REVERT: A 956 MET cc_start: 0.9317 (tpp) cc_final: 0.8865 (tpp) REVERT: A 994 MET cc_start: 0.9284 (tpp) cc_final: 0.8672 (tpp) REVERT: A 1031 MET cc_start: 0.9172 (tpp) cc_final: 0.8685 (tpp) REVERT: A 1033 GLU cc_start: 0.9166 (mp0) cc_final: 0.8884 (mp0) REVERT: A 1078 MET cc_start: 0.9298 (pmm) cc_final: 0.9075 (pmm) REVERT: A 1146 LEU cc_start: 0.8880 (mt) cc_final: 0.8597 (mt) REVERT: A 1199 LEU cc_start: 0.9151 (mt) cc_final: 0.8810 (mt) REVERT: A 1364 MET cc_start: 0.9297 (mmm) cc_final: 0.8454 (mmm) REVERT: A 1477 MET cc_start: 0.9298 (tpt) cc_final: 0.8488 (tpp) REVERT: A 1512 MET cc_start: 0.8980 (ppp) cc_final: 0.8441 (ppp) REVERT: A 1578 MET cc_start: 0.8789 (tpp) cc_final: 0.8404 (tpp) REVERT: A 1598 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 1599 LEU cc_start: 0.9666 (tp) cc_final: 0.9428 (tt) REVERT: A 1634 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 1650 MET cc_start: 0.8465 (mmp) cc_final: 0.8246 (mmp) REVERT: A 1717 MET cc_start: 0.9260 (tpt) cc_final: 0.8789 (tpp) REVERT: A 1761 LEU cc_start: 0.9242 (mt) cc_final: 0.8916 (mt) REVERT: A 2010 MET cc_start: 0.9042 (mmt) cc_final: 0.8649 (mmt) REVERT: A 2011 MET cc_start: 0.9497 (tmm) cc_final: 0.9214 (tmm) REVERT: A 2026 MET cc_start: 0.9433 (mtp) cc_final: 0.9042 (mtt) REVERT: A 2029 GLU cc_start: 0.9209 (pt0) cc_final: 0.8923 (pp20) REVERT: A 2199 MET cc_start: 0.8983 (tpp) cc_final: 0.8596 (tpp) REVERT: A 2220 LEU cc_start: 0.9561 (mt) cc_final: 0.9346 (mt) REVERT: A 2303 LEU cc_start: 0.9587 (mt) cc_final: 0.9376 (mt) REVERT: A 2327 MET cc_start: 0.9013 (tpp) cc_final: 0.8388 (tmm) REVERT: A 2357 ASP cc_start: 0.8142 (t0) cc_final: 0.7902 (t0) REVERT: A 2366 MET cc_start: 0.8684 (mmt) cc_final: 0.8463 (mmm) REVERT: A 2382 MET cc_start: 0.9004 (mmm) cc_final: 0.8770 (mmt) REVERT: A 2412 ASP cc_start: 0.9058 (m-30) cc_final: 0.8834 (p0) REVERT: A 2414 VAL cc_start: 0.9558 (t) cc_final: 0.9311 (p) REVERT: A 2526 GLU cc_start: 0.9441 (tp30) cc_final: 0.8935 (tp30) REVERT: C 67 MET cc_start: 0.8537 (mtp) cc_final: 0.8316 (mtp) REVERT: C 100 MET cc_start: 0.8416 (ppp) cc_final: 0.7934 (ppp) REVERT: C 157 LEU cc_start: 0.8491 (tt) cc_final: 0.8127 (mt) REVERT: C 293 LEU cc_start: 0.8658 (mt) cc_final: 0.8342 (mm) REVERT: E 55 MET cc_start: 0.6201 (mmm) cc_final: 0.5568 (mmm) REVERT: E 71 ASP cc_start: 0.9181 (p0) cc_final: 0.8916 (p0) REVERT: E 93 MET cc_start: 0.8442 (ptp) cc_final: 0.8023 (ptt) REVERT: E 97 LYS cc_start: 0.9115 (tptp) cc_final: 0.8748 (tppt) REVERT: E 186 MET cc_start: 0.8630 (mmm) cc_final: 0.8427 (mmm) REVERT: E 192 PHE cc_start: 0.8577 (m-80) cc_final: 0.7856 (m-80) REVERT: E 207 LYS cc_start: 0.9833 (mtmt) cc_final: 0.9579 (mtmm) REVERT: E 321 ASP cc_start: 0.9308 (m-30) cc_final: 0.8832 (p0) REVERT: E 328 LEU cc_start: 0.9513 (mt) cc_final: 0.9237 (mp) REVERT: E 567 ASN cc_start: 0.8945 (m-40) cc_final: 0.8599 (t0) REVERT: E 615 VAL cc_start: 0.9061 (t) cc_final: 0.8732 (p) REVERT: E 625 THR cc_start: 0.7457 (m) cc_final: 0.7087 (p) REVERT: E 1108 MET cc_start: 0.8381 (tpt) cc_final: 0.7411 (tpt) REVERT: E 1150 TRP cc_start: 0.6688 (m100) cc_final: 0.6262 (m100) REVERT: E 1205 MET cc_start: 0.6590 (mtt) cc_final: 0.6031 (mtp) REVERT: E 1285 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8650 (tm-30) REVERT: I 144 MET cc_start: 0.7562 (mtt) cc_final: 0.7325 (mtt) REVERT: I 166 MET cc_start: 0.8825 (mmp) cc_final: 0.8405 (tpp) REVERT: I 194 MET cc_start: 0.9538 (tpp) cc_final: 0.9116 (tpt) REVERT: I 366 MET cc_start: 0.7317 (mpp) cc_final: 0.6934 (mpp) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1897 time to fit residues: 107.5348 Evaluate side-chains 270 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 143 optimal weight: 6.9990 chunk 355 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 326 optimal weight: 0.1980 chunk 289 optimal weight: 0.0000 chunk 240 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 291 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.082559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.061689 restraints weight = 178613.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.063213 restraints weight = 97325.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064259 restraints weight = 63050.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.065046 restraints weight = 47177.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065566 restraints weight = 37679.387| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31566 Z= 0.111 Angle : 0.580 10.777 42806 Z= 0.289 Chirality : 0.040 0.222 4846 Planarity : 0.004 0.066 5459 Dihedral : 4.174 54.578 4199 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3768 helix: 1.68 (0.11), residues: 2215 sheet: -1.45 (0.25), residues: 386 loop : -0.71 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2060 TYR 0.020 0.001 TYR A2423 PHE 0.024 0.001 PHE E1060 TRP 0.085 0.001 TRP A1269 HIS 0.004 0.001 HIS A 968 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (31566) covalent geometry : angle 0.57987 / 0.29 (42806) hydrogen bonds : bond 0.03497 / 2.30 ( 1714) hydrogen bonds : angle 4.14309 / 2.86 ( 5019) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9347 (mmm) cc_final: 0.8912 (mmp) REVERT: A 813 MET cc_start: 0.8614 (ppp) cc_final: 0.7861 (ppp) REVERT: A 823 ILE cc_start: 0.9590 (mm) cc_final: 0.9367 (pt) REVERT: A 956 MET cc_start: 0.9226 (tpp) cc_final: 0.8816 (tpp) REVERT: A 994 MET cc_start: 0.9191 (tpp) cc_final: 0.8640 (tpp) REVERT: A 1031 MET cc_start: 0.9080 (tpp) cc_final: 0.8581 (tpp) REVERT: A 1033 GLU cc_start: 0.9142 (mp0) cc_final: 0.8868 (mp0) REVERT: A 1078 MET cc_start: 0.9290 (pmm) cc_final: 0.9054 (pmm) REVERT: A 1313 MET cc_start: 0.8235 (mmp) cc_final: 0.7499 (mmt) REVERT: A 1477 MET cc_start: 0.9091 (tpt) cc_final: 0.8887 (tpt) REVERT: A 1512 MET cc_start: 0.8946 (ppp) cc_final: 0.8374 (ppp) REVERT: A 1578 MET cc_start: 0.8749 (tpp) cc_final: 0.8412 (tpp) REVERT: A 1598 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 1633 TRP cc_start: 0.9175 (m100) cc_final: 0.8885 (m100) REVERT: A 1634 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8817 (tm-30) REVERT: A 1650 MET cc_start: 0.8351 (mmp) cc_final: 0.8120 (mmm) REVERT: A 1717 MET cc_start: 0.9281 (tpt) cc_final: 0.8825 (tpp) REVERT: A 1736 ASP cc_start: 0.8194 (m-30) cc_final: 0.7370 (p0) REVERT: A 1747 MET cc_start: 0.9029 (ttm) cc_final: 0.8280 (ttm) REVERT: A 1761 LEU cc_start: 0.9244 (mt) cc_final: 0.8939 (mt) REVERT: A 1804 TYR cc_start: 0.7622 (m-80) cc_final: 0.7367 (m-10) REVERT: A 2026 MET cc_start: 0.9427 (mtp) cc_final: 0.9025 (mtt) REVERT: A 2029 GLU cc_start: 0.9137 (pt0) cc_final: 0.8880 (pp20) REVERT: A 2059 GLU cc_start: 0.9420 (tt0) cc_final: 0.9204 (mt-10) REVERT: A 2195 ASP cc_start: 0.9108 (m-30) cc_final: 0.8805 (m-30) REVERT: A 2199 MET cc_start: 0.8953 (tpp) cc_final: 0.8551 (tpp) REVERT: A 2327 MET cc_start: 0.8943 (tpp) cc_final: 0.8328 (tmm) REVERT: A 2357 ASP cc_start: 0.7999 (t0) cc_final: 0.7704 (t0) REVERT: A 2366 MET cc_start: 0.8636 (mmt) cc_final: 0.8422 (mmm) REVERT: A 2382 MET cc_start: 0.9000 (mmm) cc_final: 0.8774 (mmt) REVERT: A 2414 VAL cc_start: 0.9532 (t) cc_final: 0.9262 (p) REVERT: A 2526 GLU cc_start: 0.9395 (tp30) cc_final: 0.8880 (tp30) REVERT: C 100 MET cc_start: 0.8338 (ppp) cc_final: 0.7842 (ppp) REVERT: C 106 ASP cc_start: 0.8240 (p0) cc_final: 0.8035 (p0) REVERT: C 157 LEU cc_start: 0.8467 (tt) cc_final: 0.8121 (mt) REVERT: C 293 LEU cc_start: 0.8638 (mt) cc_final: 0.8321 (mm) REVERT: E 51 MET cc_start: 0.8160 (tpp) cc_final: 0.7547 (tpp) REVERT: E 55 MET cc_start: 0.6195 (mmm) cc_final: 0.5548 (mmm) REVERT: E 71 ASP cc_start: 0.9161 (p0) cc_final: 0.8901 (p0) REVERT: E 192 PHE cc_start: 0.8510 (m-80) cc_final: 0.7857 (m-80) REVERT: E 207 LYS cc_start: 0.9829 (mtmt) cc_final: 0.9577 (mtmm) REVERT: E 328 LEU cc_start: 0.9516 (mt) cc_final: 0.9247 (mp) REVERT: E 567 ASN cc_start: 0.8905 (m-40) cc_final: 0.8554 (t0) REVERT: E 615 VAL cc_start: 0.9046 (t) cc_final: 0.8707 (p) REVERT: E 625 THR cc_start: 0.7331 (m) cc_final: 0.6955 (p) REVERT: E 1105 ASN cc_start: 0.9583 (m-40) cc_final: 0.9147 (p0) REVERT: E 1108 MET cc_start: 0.8316 (tpt) cc_final: 0.7317 (tpt) REVERT: E 1150 TRP cc_start: 0.6816 (m100) cc_final: 0.6187 (m100) REVERT: E 1205 MET cc_start: 0.6632 (mtt) cc_final: 0.5849 (ttp) REVERT: E 1285 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8626 (tm-30) REVERT: E 1324 TYR cc_start: 0.7013 (m-80) cc_final: 0.6512 (m-80) REVERT: I 144 MET cc_start: 0.7557 (mtt) cc_final: 0.7354 (mtt) REVERT: I 166 MET cc_start: 0.8770 (mmp) cc_final: 0.8344 (tpp) REVERT: I 194 MET cc_start: 0.9523 (tpp) cc_final: 0.9125 (tpt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1832 time to fit residues: 106.1397 Evaluate side-chains 266 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 316 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 346 optimal weight: 0.4980 chunk 356 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 325 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** 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 = 0.3873 r_free = 0.3873 target = 0.082285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061153 restraints weight = 179217.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.062682 restraints weight = 98199.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.063951 restraints weight = 66626.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.064678 restraints weight = 48696.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065140 restraints weight = 39475.615| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31566 Z= 0.118 Angle : 0.584 10.204 42806 Z= 0.293 Chirality : 0.040 0.289 4846 Planarity : 0.004 0.079 5459 Dihedral : 4.194 54.379 4199 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3768 helix: 1.66 (0.11), residues: 2222 sheet: -1.50 (0.25), residues: 387 loop : -0.66 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 227 TYR 0.019 0.001 TYR A2423 PHE 0.035 0.001 PHE A1103 TRP 0.045 0.001 TRP C 272 HIS 0.008 0.001 HIS A1988 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (31566) covalent geometry : angle 0.58361 / 0.29 (42806) hydrogen bonds : bond 0.03442 / 2.26 ( 1714) hydrogen bonds : angle 4.16735 / 2.89 ( 5019) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9379 (mmm) cc_final: 0.8933 (mmp) REVERT: A 813 MET cc_start: 0.8668 (ppp) cc_final: 0.7893 (ppp) REVERT: A 828 LEU cc_start: 0.9408 (tp) cc_final: 0.9203 (pp) REVERT: A 956 MET cc_start: 0.9259 (tpp) cc_final: 0.8809 (tpp) REVERT: A 994 MET cc_start: 0.9274 (tpp) cc_final: 0.8679 (tpp) REVERT: A 1031 MET cc_start: 0.9148 (tpp) cc_final: 0.8644 (tpp) REVERT: A 1033 GLU cc_start: 0.9135 (mp0) cc_final: 0.8911 (mp0) REVERT: A 1078 MET cc_start: 0.9301 (pmm) cc_final: 0.9075 (pmm) REVERT: A 1313 MET cc_start: 0.8337 (mmp) cc_final: 0.7588 (mmt) REVERT: A 1477 MET cc_start: 0.9515 (tpt) cc_final: 0.8559 (tpp) REVERT: A 1512 MET cc_start: 0.8963 (ppp) cc_final: 0.8471 (ppp) REVERT: A 1529 MET cc_start: 0.9117 (tpp) cc_final: 0.8909 (mmm) REVERT: A 1578 MET cc_start: 0.8767 (tpp) cc_final: 0.8407 (tpp) REVERT: A 1598 GLU cc_start: 0.8615 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 1634 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8845 (tm-30) REVERT: A 1650 MET cc_start: 0.8494 (mmp) cc_final: 0.8237 (mmm) REVERT: A 1736 ASP cc_start: 0.8419 (m-30) cc_final: 0.7534 (p0) REVERT: A 1747 MET cc_start: 0.9099 (ttm) cc_final: 0.8409 (ttm) REVERT: A 1761 LEU cc_start: 0.9260 (mt) cc_final: 0.8952 (mt) REVERT: A 2026 MET cc_start: 0.9447 (mtp) cc_final: 0.9043 (mtt) REVERT: A 2029 GLU cc_start: 0.9184 (pt0) cc_final: 0.8918 (pp20) REVERT: A 2059 GLU cc_start: 0.9449 (tt0) cc_final: 0.9191 (mt-10) REVERT: A 2195 ASP cc_start: 0.9143 (m-30) cc_final: 0.8842 (m-30) REVERT: A 2199 MET cc_start: 0.9049 (tpp) cc_final: 0.8619 (tpp) REVERT: A 2303 LEU cc_start: 0.9552 (mt) cc_final: 0.9344 (mt) REVERT: A 2327 MET cc_start: 0.9028 (tpp) cc_final: 0.8308 (tmm) REVERT: A 2345 MET cc_start: 0.8855 (mtp) cc_final: 0.8354 (mtm) REVERT: A 2357 ASP cc_start: 0.8038 (t0) cc_final: 0.7633 (t0) REVERT: A 2366 MET cc_start: 0.8670 (mmt) cc_final: 0.8459 (mmm) REVERT: A 2382 MET cc_start: 0.9042 (mmm) cc_final: 0.8800 (mmt) REVERT: A 2414 VAL cc_start: 0.9533 (t) cc_final: 0.9268 (p) REVERT: A 2526 GLU cc_start: 0.9435 (tp30) cc_final: 0.8903 (tp30) REVERT: C 100 MET cc_start: 0.8322 (ppp) cc_final: 0.7816 (ppp) REVERT: C 157 LEU cc_start: 0.8405 (tt) cc_final: 0.8069 (mt) REVERT: C 273 MET cc_start: 0.7399 (ppp) cc_final: 0.7198 (ppp) REVERT: C 293 LEU cc_start: 0.8616 (mt) cc_final: 0.8312 (mm) REVERT: E 51 MET cc_start: 0.8096 (tpp) cc_final: 0.7453 (tpp) REVERT: E 55 MET cc_start: 0.6138 (mmm) cc_final: 0.5495 (mmm) REVERT: E 71 ASP cc_start: 0.9140 (p0) cc_final: 0.8883 (p0) REVERT: E 93 MET cc_start: 0.8421 (ptt) cc_final: 0.8117 (ppp) REVERT: E 192 PHE cc_start: 0.8322 (m-80) cc_final: 0.7784 (m-80) REVERT: E 328 LEU cc_start: 0.9514 (mt) cc_final: 0.9251 (mp) REVERT: E 567 ASN cc_start: 0.8950 (m-40) cc_final: 0.8623 (t0) REVERT: E 615 VAL cc_start: 0.9051 (t) cc_final: 0.8740 (p) REVERT: E 625 THR cc_start: 0.7350 (m) cc_final: 0.6983 (p) REVERT: E 1028 VAL cc_start: 0.6324 (p) cc_final: 0.6081 (p) REVERT: E 1105 ASN cc_start: 0.9636 (m-40) cc_final: 0.9229 (p0) REVERT: E 1108 MET cc_start: 0.8560 (tpt) cc_final: 0.8193 (tpt) REVERT: E 1150 TRP cc_start: 0.6712 (m100) cc_final: 0.6176 (m100) REVERT: E 1205 MET cc_start: 0.6511 (mtt) cc_final: 0.5706 (ttp) REVERT: E 1285 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8629 (tm-30) REVERT: E 1324 TYR cc_start: 0.6980 (m-80) cc_final: 0.6541 (m-80) REVERT: I 166 MET cc_start: 0.8797 (mmp) cc_final: 0.8372 (tpp) REVERT: I 194 MET cc_start: 0.9522 (tpp) cc_final: 0.9126 (tpt) REVERT: I 228 MET cc_start: 0.7416 (pmm) cc_final: 0.6435 (mmm) REVERT: I 366 MET cc_start: 0.6870 (mpp) cc_final: 0.6158 (mpp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1771 time to fit residues: 100.7921 Evaluate side-chains 267 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 332 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 239 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 337 optimal weight: 0.7980 chunk 219 optimal weight: 0.5980 chunk 334 optimal weight: 0.4980 chunk 328 optimal weight: 0.0870 chunk 381 optimal weight: 0.0470 chunk 189 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN ** I 191 HIS ** 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 = 0.3890 r_free = 0.3890 target = 0.083058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.062186 restraints weight = 178842.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063653 restraints weight = 96277.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.064743 restraints weight = 62771.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065492 restraints weight = 46019.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.065866 restraints weight = 37275.854| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31566 Z= 0.110 Angle : 0.580 9.734 42806 Z= 0.289 Chirality : 0.040 0.179 4846 Planarity : 0.004 0.073 5459 Dihedral : 4.143 54.256 4199 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3768 helix: 1.70 (0.11), residues: 2216 sheet: -1.32 (0.26), residues: 367 loop : -0.71 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 814 TYR 0.016 0.001 TYR A2423 PHE 0.026 0.001 PHE A1103 TRP 0.074 0.001 TRP A1269 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (31566) covalent geometry : angle 0.57995 / 0.29 (42806) hydrogen bonds : bond 0.03326 / 2.19 ( 1714) hydrogen bonds : angle 4.10522 / 2.84 ( 5019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5951.12 seconds wall clock time: 103 minutes 40.68 seconds (6220.68 seconds total)