Starting phenix.real_space_refine on Fri Mar 6 14:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pec_13352/03_2026/7pec_13352.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pec_13352/03_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_13352/03_2026/7pec_13352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pec_13352/03_2026/7pec_13352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pec_13352/03_2026/7pec_13352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pec_13352/03_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-5986/lib/python3.9/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: 6.21, 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: 2.32 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: 1.52 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: 7.82 Time building geometry restraints manager: 3.07 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: 17173 17.25 - 34.50: 1434 34.50 - 51.75: 379 51.75 - 69.01: 99 69.01 - 86.26: 20 Dihedral angle restraints: 19105 sinusoidal: 7757 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 19102 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: 7.020 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: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 28.850 Find NCS groups from input model: 0.150 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 14.484 86.257 11709 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 covalent geometry : bond 0.00226 (31566) covalent geometry : angle 0.48537 (42806) hydrogen bonds : bond 0.24290 ( 1714) hydrogen bonds : angle 7.46547 ( 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 : 1.209 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: 0.2035 time to fit residues: 256.2169 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 : 1.588 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 166 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN 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 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 = 0.083535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062493 restraints weight = 174807.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.064207 restraints weight = 96887.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065275 restraints weight = 62125.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065976 restraints weight = 45073.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.066295 restraints weight = 36183.676| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31566 Z= 0.156 Angle : 0.654 11.838 42806 Z= 0.339 Chirality : 0.043 0.199 4846 Planarity : 0.005 0.059 5459 Dihedral : 4.576 49.495 4235 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 3768 helix: 0.94 (0.10), residues: 2199 sheet: -2.85 (0.22), residues: 375 loop : -0.96 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2378 TYR 0.025 0.002 TYR E1324 PHE 0.027 0.002 PHE I 371 TRP 0.029 0.002 TRP C 112 HIS 0.010 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00332 (31566) covalent geometry : angle 0.65375 (42806) hydrogen bonds : bond 0.05664 ( 1714) hydrogen bonds : angle 5.02771 ( 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 455 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 451 time to evaluate : 1.221 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: 0.9383 (mmm) cc_final: 0.8957 (mmm) REVERT: A 772 MET cc_start: 0.8695 (tmm) cc_final: 0.8441 (tmm) REVERT: A 822 ILE cc_start: 0.9670 (mt) cc_final: 0.9274 (tp) REVERT: A 824 ILE cc_start: 0.9727 (mt) cc_final: 0.9466 (tp) REVERT: A 827 MET cc_start: 0.9006 (tmm) cc_final: 0.8726 (tmm) REVERT: A 828 LEU cc_start: 0.9344 (mt) cc_final: 0.8898 (mt) REVERT: A 956 MET cc_start: 0.9266 (tpp) cc_final: 0.8664 (tpp) REVERT: A 994 MET cc_start: 0.9061 (tpp) cc_final: 0.8542 (tpp) REVERT: A 1031 MET cc_start: 0.9200 (tpp) cc_final: 0.8745 (tpp) REVERT: A 1033 GLU cc_start: 0.9139 (mp0) cc_final: 0.8859 (mp0) REVERT: A 1035 VAL cc_start: 0.9677 (p) cc_final: 0.9454 (p) REVERT: A 1146 LEU cc_start: 0.8964 (mt) cc_final: 0.8633 (mt) REVERT: A 1477 MET cc_start: 0.9328 (ttp) cc_final: 0.8917 (tpp) REVERT: A 1481 MET cc_start: 0.8815 (mtm) cc_final: 0.8524 (ptp) REVERT: A 1549 VAL cc_start: 0.9630 (t) cc_final: 0.9402 (t) REVERT: A 1596 LEU cc_start: 0.9693 (mt) cc_final: 0.9451 (mt) REVERT: A 1598 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 1601 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 1632 ASP cc_start: 0.8830 (m-30) cc_final: 0.8606 (m-30) REVERT: A 1650 MET cc_start: 0.8250 (mmt) cc_final: 0.7883 (mmm) REVERT: A 1743 LEU cc_start: 0.9098 (tt) cc_final: 0.8691 (tp) REVERT: A 1747 MET cc_start: 0.8727 (ttm) cc_final: 0.8252 (ttm) REVERT: A 1753 LYS cc_start: 0.9565 (mmtt) cc_final: 0.9283 (mmmm) REVERT: A 1760 ASN cc_start: 0.9314 (m-40) cc_final: 0.9056 (t0) REVERT: A 1900 LEU cc_start: 0.9440 (tp) cc_final: 0.9212 (tt) REVERT: A 1930 ILE cc_start: 0.9031 (tt) cc_final: 0.8823 (tt) REVERT: A 1964 ILE cc_start: 0.9490 (mm) cc_final: 0.8981 (tp) REVERT: A 2026 MET cc_start: 0.9465 (mtp) cc_final: 0.9110 (mtp) REVERT: A 2029 GLU cc_start: 0.9095 (pt0) cc_final: 0.8795 (pp20) REVERT: A 2327 MET cc_start: 0.8821 (tpt) cc_final: 0.8517 (tpt) REVERT: A 2329 MET cc_start: 0.9406 (mmp) cc_final: 0.9150 (mmm) REVERT: A 2382 MET cc_start: 0.8732 (mmm) cc_final: 0.8488 (mmt) REVERT: A 2412 ASP cc_start: 0.9068 (m-30) cc_final: 0.8713 (p0) REVERT: A 2526 GLU cc_start: 0.9258 (tp30) cc_final: 0.8869 (tp30) REVERT: C 143 LEU cc_start: 0.9437 (tp) cc_final: 0.9166 (tt) REVERT: C 255 MET cc_start: 0.8722 (ttp) cc_final: 0.8475 (tmm) REVERT: C 273 MET cc_start: 0.8419 (ttp) cc_final: 0.7058 (ppp) REVERT: C 293 LEU cc_start: 0.8776 (mt) cc_final: 0.8450 (mm) REVERT: E 51 MET cc_start: 0.8342 (tpp) cc_final: 0.8069 (tpp) REVERT: E 71 ASP cc_start: 0.9152 (p0) cc_final: 0.8893 (p0) REVERT: E 186 MET cc_start: 0.8534 (mmm) cc_final: 0.8201 (mmm) REVERT: E 192 PHE cc_start: 0.8820 (m-80) cc_final: 0.8216 (m-80) REVERT: E 328 LEU cc_start: 0.9527 (mt) cc_final: 0.9248 (mp) REVERT: E 351 LEU cc_start: 0.9403 (mt) cc_final: 0.8974 (mt) REVERT: E 534 MET cc_start: 0.8520 (mtt) cc_final: 0.8290 (mtt) REVERT: E 567 ASN cc_start: 0.9078 (m-40) cc_final: 0.8618 (t0) REVERT: E 625 THR cc_start: 0.7637 (m) cc_final: 0.7354 (p) REVERT: E 961 ASP cc_start: 0.8898 (t70) cc_final: 0.8502 (t0) REVERT: E 1055 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7973 (pm20) REVERT: E 1150 TRP cc_start: 0.6410 (m100) cc_final: 0.6147 (m100) REVERT: E 1205 MET cc_start: 0.6831 (mtt) cc_final: 0.5814 (ttm) REVERT: E 1285 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8606 (tm-30) REVERT: I 144 MET cc_start: 0.7418 (mtt) cc_final: 0.7072 (mtt) REVERT: I 194 MET cc_start: 0.9457 (tpp) cc_final: 0.9067 (tpt) REVERT: I 369 CYS cc_start: 0.8474 (m) cc_final: 0.8192 (m) outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.1921 time to fit residues: 140.7055 Evaluate side-chains 317 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 30.0000 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 361 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** E 151 ASN E 198 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 601 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.081705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061045 restraints weight = 176964.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062611 restraints weight = 98032.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.063564 restraints weight = 63471.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.064445 restraints weight = 46749.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064968 restraints weight = 37763.244| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31566 Z= 0.170 Angle : 0.618 9.731 42806 Z= 0.318 Chirality : 0.042 0.218 4846 Planarity : 0.005 0.060 5459 Dihedral : 4.517 50.993 4235 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % 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: 0.26 (0.14), residues: 3768 helix: 1.28 (0.11), residues: 2213 sheet: -2.48 (0.23), residues: 379 loop : -0.94 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1094 TYR 0.031 0.002 TYR E1324 PHE 0.022 0.002 PHE A1122 TRP 0.070 0.002 TRP A1269 HIS 0.009 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00365 (31566) covalent geometry : angle 0.61790 (42806) hydrogen bonds : bond 0.04803 ( 1714) hydrogen bonds : angle 4.76199 ( 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: 2 poor density : 385 time to evaluate : 1.170 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 277 MET cc_start: -0.3760 (mmt) cc_final: -0.3965 (mtt) REVERT: A 733 MET cc_start: 0.9393 (mmm) cc_final: 0.8962 (mmp) REVERT: A 822 ILE cc_start: 0.9693 (mt) cc_final: 0.9306 (tp) REVERT: A 824 ILE cc_start: 0.9740 (mt) cc_final: 0.9480 (tp) REVERT: A 828 LEU cc_start: 0.9355 (mt) cc_final: 0.8962 (mt) REVERT: A 956 MET cc_start: 0.9370 (tpp) cc_final: 0.8838 (tpp) REVERT: A 994 MET cc_start: 0.9172 (tpp) cc_final: 0.8649 (tpp) REVERT: A 1031 MET cc_start: 0.9184 (tpp) cc_final: 0.8733 (tpp) REVERT: A 1033 GLU cc_start: 0.9239 (mp0) cc_final: 0.8920 (mp0) REVERT: A 1074 LEU cc_start: 0.9739 (mp) cc_final: 0.9509 (mp) REVERT: A 1146 LEU cc_start: 0.8994 (mt) cc_final: 0.8700 (mt) REVERT: A 1199 LEU cc_start: 0.9428 (mt) cc_final: 0.9060 (mt) REVERT: A 1313 MET cc_start: 0.8359 (mmp) cc_final: 0.8065 (mmt) REVERT: A 1364 MET cc_start: 0.9177 (mmm) cc_final: 0.8669 (mmm) REVERT: A 1467 MET cc_start: 0.9002 (mtp) cc_final: 0.8541 (mtp) REVERT: A 1477 MET cc_start: 0.9315 (ttp) cc_final: 0.8961 (tpp) REVERT: A 1481 MET cc_start: 0.8854 (mtm) cc_final: 0.8583 (ptp) REVERT: A 1598 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 1601 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 1632 ASP cc_start: 0.8818 (m-30) cc_final: 0.8601 (m-30) REVERT: A 1634 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 1638 MET cc_start: 0.8243 (mmp) cc_final: 0.7939 (mmp) REVERT: A 1650 MET cc_start: 0.8077 (mmt) cc_final: 0.7740 (mmm) REVERT: A 1719 HIS cc_start: 0.9003 (m-70) cc_final: 0.8615 (m-70) REVERT: A 1724 MET cc_start: 0.8767 (mtm) cc_final: 0.8322 (mtp) REVERT: A 1761 LEU cc_start: 0.9186 (mt) cc_final: 0.8967 (mt) REVERT: A 1804 TYR cc_start: 0.7766 (m-80) cc_final: 0.7497 (m-10) REVERT: A 1964 ILE cc_start: 0.9466 (mm) cc_final: 0.8860 (tp) REVERT: A 2026 MET cc_start: 0.9466 (mtp) cc_final: 0.9079 (mtt) REVERT: A 2029 GLU cc_start: 0.9144 (pt0) cc_final: 0.8822 (pp20) REVERT: A 2199 MET cc_start: 0.8775 (tpp) cc_final: 0.8487 (tpp) REVERT: A 2271 MET cc_start: 0.9134 (tpp) cc_final: 0.8917 (tpp) REVERT: A 2303 LEU cc_start: 0.9602 (mt) cc_final: 0.9367 (mt) REVERT: A 2382 MET cc_start: 0.8877 (mmm) cc_final: 0.8632 (mmt) REVERT: A 2412 ASP cc_start: 0.9045 (m-30) cc_final: 0.8776 (p0) REVERT: A 2415 MET cc_start: 0.9121 (tpp) cc_final: 0.8753 (tpp) REVERT: A 2506 ASP cc_start: 0.8777 (t0) cc_final: 0.8574 (t0) REVERT: A 2526 GLU cc_start: 0.9385 (tp30) cc_final: 0.8839 (tp30) REVERT: C 100 MET cc_start: 0.8541 (ppp) cc_final: 0.8079 (ppp) REVERT: C 273 MET cc_start: 0.8121 (ttp) cc_final: 0.7073 (ppp) REVERT: C 293 LEU cc_start: 0.8746 (mt) cc_final: 0.8452 (mm) REVERT: E 51 MET cc_start: 0.8445 (tpp) cc_final: 0.7907 (tpp) REVERT: E 71 ASP cc_start: 0.9149 (p0) cc_final: 0.8873 (p0) REVERT: E 97 LYS cc_start: 0.9313 (tptp) cc_final: 0.8728 (tppt) REVERT: E 186 MET cc_start: 0.8468 (mmm) cc_final: 0.8233 (mmm) REVERT: E 192 PHE cc_start: 0.8890 (m-80) cc_final: 0.8223 (m-80) REVERT: E 207 LYS cc_start: 0.9837 (mtmt) cc_final: 0.9622 (mttp) REVERT: E 254 MET cc_start: 0.8905 (tpp) cc_final: 0.8550 (tpp) REVERT: E 328 LEU cc_start: 0.9526 (mt) cc_final: 0.9236 (mp) REVERT: E 534 MET cc_start: 0.8454 (mtt) cc_final: 0.8232 (mtt) REVERT: E 567 ASN cc_start: 0.9004 (m-40) cc_final: 0.8623 (t0) REVERT: E 615 VAL cc_start: 0.9115 (t) cc_final: 0.8761 (p) REVERT: E 625 THR cc_start: 0.7318 (m) cc_final: 0.7042 (p) REVERT: E 659 VAL cc_start: 0.8291 (t) cc_final: 0.8080 (t) REVERT: E 1055 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7939 (pm20) REVERT: E 1108 MET cc_start: 0.8569 (tpt) cc_final: 0.7609 (tpt) REVERT: E 1150 TRP cc_start: 0.6655 (m100) cc_final: 0.6446 (m100) REVERT: E 1205 MET cc_start: 0.7016 (mtt) cc_final: 0.5983 (ttm) REVERT: E 1285 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8621 (tm-30) REVERT: E 1324 TYR cc_start: 0.7022 (m-80) cc_final: 0.6802 (m-80) REVERT: I 144 MET cc_start: 0.7407 (mtt) cc_final: 0.6984 (mtt) REVERT: I 194 MET cc_start: 0.9515 (tpp) cc_final: 0.9087 (tpt) REVERT: I 355 VAL cc_start: 0.8615 (t) cc_final: 0.8309 (t) REVERT: I 366 MET cc_start: 0.7366 (mpp) cc_final: 0.7119 (mpp) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.1918 time to fit residues: 119.9472 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 : 1.146 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 0.0000 chunk 33 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1001 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.081949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061360 restraints weight = 178040.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063028 restraints weight = 98698.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.063997 restraints weight = 64155.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064652 restraints weight = 48012.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.065095 restraints weight = 38994.919| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31566 Z= 0.137 Angle : 0.580 11.810 42806 Z= 0.294 Chirality : 0.041 0.226 4846 Planarity : 0.004 0.063 5459 Dihedral : 4.426 50.943 4235 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.50 (0.14), residues: 3768 helix: 1.47 (0.11), residues: 2216 sheet: -2.24 (0.24), residues: 366 loop : -0.90 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1094 TYR 0.025 0.001 TYR A2423 PHE 0.023 0.001 PHE A1122 TRP 0.061 0.001 TRP A1269 HIS 0.007 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00294 (31566) covalent geometry : angle 0.58038 (42806) hydrogen bonds : bond 0.04281 ( 1714) hydrogen bonds : angle 4.55702 ( 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 368 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.217 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: A 277 MET cc_start: -0.3747 (mmt) cc_final: -0.3956 (mtt) REVERT: A 733 MET cc_start: 0.9379 (mmm) cc_final: 0.8947 (mmp) REVERT: A 813 MET cc_start: 0.8469 (ppp) cc_final: 0.8060 (ppp) REVERT: A 822 ILE cc_start: 0.9631 (mt) cc_final: 0.9375 (mt) REVERT: A 956 MET cc_start: 0.9346 (tpp) cc_final: 0.8864 (tpp) REVERT: A 994 MET cc_start: 0.9127 (tpp) cc_final: 0.8633 (tpp) REVERT: A 1031 MET cc_start: 0.9151 (tpp) cc_final: 0.8742 (tpp) REVERT: A 1032 ASP cc_start: 0.9274 (p0) cc_final: 0.8884 (p0) REVERT: A 1033 GLU cc_start: 0.9239 (mp0) cc_final: 0.8825 (mp0) REVERT: A 1074 LEU cc_start: 0.9684 (mp) cc_final: 0.9470 (mp) REVERT: A 1078 MET cc_start: 0.9255 (pmm) cc_final: 0.9017 (pmm) REVERT: A 1146 LEU cc_start: 0.8967 (mt) cc_final: 0.8656 (mt) REVERT: A 1199 LEU cc_start: 0.9198 (mt) cc_final: 0.8970 (mt) REVERT: A 1313 MET cc_start: 0.8340 (mmp) cc_final: 0.8068 (mmt) REVERT: A 1364 MET cc_start: 0.9201 (mmm) cc_final: 0.8444 (mmm) REVERT: A 1467 MET cc_start: 0.9024 (mtp) cc_final: 0.8528 (mtp) REVERT: A 1477 MET cc_start: 0.9360 (ttp) cc_final: 0.8970 (tpp) REVERT: A 1481 MET cc_start: 0.8893 (mtm) cc_final: 0.8538 (ptp) REVERT: A 1549 VAL cc_start: 0.9625 (t) cc_final: 0.9402 (t) REVERT: A 1598 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 1601 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 1634 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8785 (tm-30) REVERT: A 1650 MET cc_start: 0.7990 (mmt) cc_final: 0.7699 (mmm) REVERT: A 1719 HIS cc_start: 0.8908 (m-70) cc_final: 0.8527 (m-70) REVERT: A 1724 MET cc_start: 0.8749 (mtm) cc_final: 0.8379 (mtp) REVERT: A 1761 LEU cc_start: 0.9226 (mt) cc_final: 0.8953 (mt) REVERT: A 1804 TYR cc_start: 0.7701 (m-80) cc_final: 0.7431 (m-10) REVERT: A 2026 MET cc_start: 0.9460 (mtp) cc_final: 0.9082 (mtt) REVERT: A 2029 GLU cc_start: 0.9142 (pt0) cc_final: 0.8852 (pp20) REVERT: A 2199 MET cc_start: 0.8744 (tpp) cc_final: 0.8471 (tpp) REVERT: A 2303 LEU cc_start: 0.9585 (mt) cc_final: 0.9363 (mt) REVERT: A 2346 LEU cc_start: 0.9333 (tt) cc_final: 0.9086 (tt) REVERT: A 2357 ASP cc_start: 0.8113 (t0) cc_final: 0.7840 (t0) REVERT: A 2382 MET cc_start: 0.8889 (mmm) cc_final: 0.8658 (mmt) REVERT: A 2412 ASP cc_start: 0.9022 (m-30) cc_final: 0.8789 (p0) REVERT: A 2506 ASP cc_start: 0.8756 (t0) cc_final: 0.8547 (t0) REVERT: A 2526 GLU cc_start: 0.9384 (tp30) cc_final: 0.8856 (tp30) REVERT: C 100 MET cc_start: 0.8529 (ppp) cc_final: 0.7988 (ppp) REVERT: C 255 MET cc_start: 0.8324 (tmm) cc_final: 0.8069 (tmm) REVERT: C 273 MET cc_start: 0.8002 (ttp) cc_final: 0.7182 (ppp) REVERT: C 293 LEU cc_start: 0.8711 (mt) cc_final: 0.8421 (mm) REVERT: E 51 MET cc_start: 0.8433 (tpp) cc_final: 0.7860 (tpp) REVERT: E 55 MET cc_start: 0.6074 (mmm) cc_final: 0.5839 (mmm) REVERT: E 71 ASP cc_start: 0.9137 (p0) cc_final: 0.8867 (p0) REVERT: E 93 MET cc_start: 0.8253 (ptp) cc_final: 0.7986 (ptp) REVERT: E 97 LYS cc_start: 0.9155 (tptp) cc_final: 0.8910 (tppt) REVERT: E 192 PHE cc_start: 0.8820 (m-80) cc_final: 0.8161 (m-80) REVERT: E 207 LYS cc_start: 0.9840 (mtmt) cc_final: 0.9581 (mtmm) REVERT: E 254 MET cc_start: 0.9015 (tpp) cc_final: 0.8624 (tpp) REVERT: E 328 LEU cc_start: 0.9534 (mt) cc_final: 0.9247 (mp) REVERT: E 567 ASN cc_start: 0.9023 (m-40) cc_final: 0.8653 (t0) REVERT: E 615 VAL cc_start: 0.9013 (t) cc_final: 0.8678 (p) REVERT: E 625 THR cc_start: 0.7216 (m) cc_final: 0.6971 (p) REVERT: E 967 PHE cc_start: 0.7783 (m-10) cc_final: 0.7473 (m-10) REVERT: E 1055 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8060 (pm20) REVERT: E 1108 MET cc_start: 0.8642 (tpt) cc_final: 0.7904 (tpt) REVERT: E 1150 TRP cc_start: 0.6570 (m100) cc_final: 0.6207 (m100) REVERT: E 1205 MET cc_start: 0.6856 (mtt) cc_final: 0.5830 (ttp) REVERT: E 1285 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8651 (tm-30) REVERT: I 144 MET cc_start: 0.7496 (mtt) cc_final: 0.7104 (mtt) REVERT: I 194 MET cc_start: 0.9535 (tpp) cc_final: 0.9113 (tpt) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1876 time to fit residues: 113.3690 Evaluate side-chains 284 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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: 0.6980 chunk 308 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.0040 chunk 378 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.082690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.061704 restraints weight = 176489.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.063428 restraints weight = 95625.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064605 restraints weight = 62275.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.065245 restraints weight = 45722.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.065781 restraints weight = 37446.688| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31566 Z= 0.114 Angle : 0.556 7.473 42806 Z= 0.281 Chirality : 0.040 0.233 4846 Planarity : 0.004 0.064 5459 Dihedral : 4.336 51.064 4235 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 0.64 (0.14), residues: 3768 helix: 1.55 (0.11), residues: 2224 sheet: -1.96 (0.25), residues: 378 loop : -0.87 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 616 TYR 0.018 0.001 TYR A2332 PHE 0.033 0.001 PHE A 434 TRP 0.068 0.001 TRP A1269 HIS 0.007 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00242 (31566) covalent geometry : angle 0.55586 (42806) hydrogen bonds : bond 0.03923 ( 1714) hydrogen bonds : angle 4.33651 ( 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 363 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.131 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: A 733 MET cc_start: 0.9388 (mmm) cc_final: 0.8951 (mmp) REVERT: A 813 MET cc_start: 0.8458 (ppp) cc_final: 0.7640 (ppp) REVERT: A 956 MET cc_start: 0.9317 (tpp) cc_final: 0.8846 (tpp) REVERT: A 994 MET cc_start: 0.9161 (tpp) cc_final: 0.8665 (tpp) REVERT: A 1031 MET cc_start: 0.9156 (tpp) cc_final: 0.8720 (tpp) REVERT: A 1032 ASP cc_start: 0.9282 (p0) cc_final: 0.8967 (p0) REVERT: A 1033 GLU cc_start: 0.9184 (mp0) cc_final: 0.8812 (mp0) REVERT: A 1071 LEU cc_start: 0.9569 (tp) cc_final: 0.9345 (tp) REVERT: A 1074 LEU cc_start: 0.9706 (mp) cc_final: 0.9460 (mp) REVERT: A 1078 MET cc_start: 0.9332 (pmm) cc_final: 0.9003 (pmm) REVERT: A 1146 LEU cc_start: 0.8948 (mt) cc_final: 0.8657 (mt) REVERT: A 1364 MET cc_start: 0.9233 (mmm) cc_final: 0.8459 (mmm) REVERT: A 1452 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8797 (pttm) REVERT: A 1467 MET cc_start: 0.8980 (mtp) cc_final: 0.8611 (mtp) REVERT: A 1477 MET cc_start: 0.9355 (ttp) cc_final: 0.8985 (tpp) REVERT: A 1481 MET cc_start: 0.8729 (mtm) cc_final: 0.8498 (ptp) REVERT: A 1596 LEU cc_start: 0.9682 (mt) cc_final: 0.9435 (mt) REVERT: A 1598 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 1601 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 1632 ASP cc_start: 0.8907 (m-30) cc_final: 0.8667 (m-30) REVERT: A 1634 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8828 (tm-30) REVERT: A 1650 MET cc_start: 0.7985 (mmt) cc_final: 0.7700 (mmm) REVERT: A 1719 HIS cc_start: 0.8957 (m-70) cc_final: 0.8542 (m-70) REVERT: A 1724 MET cc_start: 0.8732 (mtm) cc_final: 0.8371 (mtp) REVERT: A 1747 MET cc_start: 0.9162 (ttm) cc_final: 0.8898 (ttt) REVERT: A 1761 LEU cc_start: 0.9177 (mt) cc_final: 0.8884 (mt) REVERT: A 1804 TYR cc_start: 0.7670 (m-80) cc_final: 0.7439 (m-10) REVERT: A 1879 MET cc_start: 0.8885 (ptp) cc_final: 0.8679 (ptp) REVERT: A 2014 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8771 (tm-30) REVERT: A 2026 MET cc_start: 0.9448 (mtp) cc_final: 0.9068 (mtt) REVERT: A 2029 GLU cc_start: 0.9126 (pt0) cc_final: 0.8850 (pp20) REVERT: A 2058 MET cc_start: 0.8822 (mtm) cc_final: 0.8592 (mtp) REVERT: A 2199 MET cc_start: 0.8758 (tpp) cc_final: 0.8458 (tpp) REVERT: A 2327 MET cc_start: 0.9128 (tpp) cc_final: 0.8322 (tmm) REVERT: A 2357 ASP cc_start: 0.8103 (t0) cc_final: 0.7830 (t0) REVERT: A 2382 MET cc_start: 0.8953 (mmm) cc_final: 0.8730 (mmt) REVERT: A 2412 ASP cc_start: 0.9009 (m-30) cc_final: 0.8806 (p0) REVERT: A 2415 MET cc_start: 0.9101 (tpp) cc_final: 0.8873 (tpp) REVERT: A 2506 ASP cc_start: 0.8786 (t0) cc_final: 0.8560 (t0) REVERT: A 2526 GLU cc_start: 0.9414 (tp30) cc_final: 0.8887 (tp30) REVERT: C 255 MET cc_start: 0.8261 (tmm) cc_final: 0.8039 (tmm) REVERT: C 273 MET cc_start: 0.7934 (ttp) cc_final: 0.7200 (ppp) REVERT: E 51 MET cc_start: 0.8459 (tpp) cc_final: 0.7935 (tpp) REVERT: E 55 MET cc_start: 0.6181 (mmm) cc_final: 0.5893 (mmm) REVERT: E 71 ASP cc_start: 0.9124 (p0) cc_final: 0.8863 (p0) REVERT: E 192 PHE cc_start: 0.8640 (m-80) cc_final: 0.8073 (m-80) REVERT: E 207 LYS cc_start: 0.9832 (mtmt) cc_final: 0.9567 (mtmm) REVERT: E 254 MET cc_start: 0.9162 (tpp) cc_final: 0.8781 (tpp) REVERT: E 328 LEU cc_start: 0.9507 (mt) cc_final: 0.9223 (mp) REVERT: E 567 ASN cc_start: 0.8951 (m-40) cc_final: 0.8569 (t0) REVERT: E 615 VAL cc_start: 0.8974 (t) cc_final: 0.8625 (p) REVERT: E 625 THR cc_start: 0.7172 (m) cc_final: 0.6945 (p) REVERT: E 1055 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8022 (pm20) REVERT: E 1108 MET cc_start: 0.8491 (tpt) cc_final: 0.8010 (tpt) REVERT: E 1150 TRP cc_start: 0.6507 (m100) cc_final: 0.6097 (m100) REVERT: E 1205 MET cc_start: 0.6737 (mtt) cc_final: 0.5871 (ttm) REVERT: E 1285 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8623 (tm-30) REVERT: I 144 MET cc_start: 0.7444 (mtt) cc_final: 0.7112 (mtt) REVERT: I 194 MET cc_start: 0.9521 (tpp) cc_final: 0.9121 (tpt) REVERT: I 366 MET cc_start: 0.7305 (mpp) cc_final: 0.6876 (mpp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1829 time to fit residues: 110.0240 Evaluate side-chains 281 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 1.9990 chunk 370 optimal weight: 0.0270 chunk 237 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 271 optimal weight: 0.0060 chunk 0 optimal weight: 50.0000 chunk 151 optimal weight: 2.9990 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 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 = 0.3889 r_free = 0.3889 target = 0.082904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061875 restraints weight = 177937.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.063660 restraints weight = 95530.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064835 restraints weight = 61691.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.065431 restraints weight = 44862.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065907 restraints weight = 36779.955| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31566 Z= 0.111 Angle : 0.552 9.514 42806 Z= 0.277 Chirality : 0.040 0.221 4846 Planarity : 0.004 0.064 5459 Dihedral : 4.256 51.582 4235 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 0.78 (0.14), residues: 3768 helix: 1.65 (0.11), residues: 2217 sheet: -1.72 (0.25), residues: 380 loop : -0.83 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 616 TYR 0.019 0.001 TYR A1151 PHE 0.022 0.001 PHE A1122 TRP 0.070 0.001 TRP A1269 HIS 0.006 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00237 (31566) covalent geometry : angle 0.55231 (42806) hydrogen bonds : bond 0.03685 ( 1714) hydrogen bonds : angle 4.23504 ( 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 356 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.938 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 311 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8260 (tpp80) REVERT: A 733 MET cc_start: 0.9385 (mmm) cc_final: 0.8935 (mmp) REVERT: A 756 MET cc_start: 0.7501 (mmt) cc_final: 0.7034 (mmm) REVERT: A 813 MET cc_start: 0.8470 (ppp) cc_final: 0.7739 (ppp) REVERT: A 956 MET cc_start: 0.9305 (tpp) cc_final: 0.8846 (tpp) REVERT: A 994 MET cc_start: 0.9162 (tpp) cc_final: 0.8654 (tpp) REVERT: A 1031 MET cc_start: 0.9165 (tpp) cc_final: 0.8719 (tpp) REVERT: A 1033 GLU cc_start: 0.9151 (mp0) cc_final: 0.8864 (mp0) REVERT: A 1146 LEU cc_start: 0.8932 (mt) cc_final: 0.8660 (mt) REVERT: A 1199 LEU cc_start: 0.9219 (mt) cc_final: 0.8936 (mt) REVERT: A 1364 MET cc_start: 0.9240 (mmm) cc_final: 0.8431 (mmm) REVERT: A 1467 MET cc_start: 0.8976 (mtp) cc_final: 0.8655 (mtp) REVERT: A 1477 MET cc_start: 0.9333 (ttp) cc_final: 0.8961 (tpp) REVERT: A 1598 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 1601 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 1632 ASP cc_start: 0.8875 (m-30) cc_final: 0.8621 (m-30) REVERT: A 1634 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8885 (tm-30) REVERT: A 1650 MET cc_start: 0.7986 (mmt) cc_final: 0.7700 (mmm) REVERT: A 1719 HIS cc_start: 0.8963 (m-70) cc_final: 0.8540 (m-70) REVERT: A 1724 MET cc_start: 0.8819 (mtm) cc_final: 0.8400 (mtp) REVERT: A 1747 MET cc_start: 0.9154 (ttm) cc_final: 0.8442 (ttm) REVERT: A 1761 LEU cc_start: 0.9223 (mt) cc_final: 0.8952 (mt) REVERT: A 1804 TYR cc_start: 0.7676 (m-80) cc_final: 0.7371 (m-80) REVERT: A 2014 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8769 (tm-30) REVERT: A 2026 MET cc_start: 0.9453 (mtp) cc_final: 0.9063 (mtt) REVERT: A 2029 GLU cc_start: 0.9132 (pt0) cc_final: 0.8853 (pp20) REVERT: A 2199 MET cc_start: 0.8794 (tpp) cc_final: 0.8453 (tpp) REVERT: A 2268 MET cc_start: 0.9016 (tpp) cc_final: 0.8739 (tpp) REVERT: A 2327 MET cc_start: 0.9124 (tpp) cc_final: 0.8272 (tmm) REVERT: A 2357 ASP cc_start: 0.8055 (t0) cc_final: 0.7787 (t0) REVERT: A 2382 MET cc_start: 0.8937 (mmm) cc_final: 0.8722 (mmt) REVERT: A 2415 MET cc_start: 0.9076 (tpp) cc_final: 0.8868 (tpp) REVERT: A 2506 ASP cc_start: 0.8778 (t0) cc_final: 0.8558 (t0) REVERT: A 2526 GLU cc_start: 0.9409 (tp30) cc_final: 0.8846 (tp30) REVERT: C 86 LYS cc_start: 0.8768 (pttm) cc_final: 0.8566 (pttm) REVERT: C 100 MET cc_start: 0.8424 (ppp) cc_final: 0.7967 (ppp) REVERT: C 157 LEU cc_start: 0.8538 (tt) cc_final: 0.8307 (mp) REVERT: C 255 MET cc_start: 0.8256 (tmm) cc_final: 0.7990 (tmm) REVERT: C 293 LEU cc_start: 0.8640 (mt) cc_final: 0.8358 (mm) REVERT: E 51 MET cc_start: 0.8467 (tpp) cc_final: 0.7921 (tpp) REVERT: E 55 MET cc_start: 0.6236 (mmm) cc_final: 0.5538 (mmm) REVERT: E 71 ASP cc_start: 0.9116 (p0) cc_final: 0.8855 (p0) REVERT: E 192 PHE cc_start: 0.8373 (m-80) cc_final: 0.7835 (m-80) REVERT: E 207 LYS cc_start: 0.9831 (mtmt) cc_final: 0.9579 (mtmm) REVERT: E 254 MET cc_start: 0.9193 (tpp) cc_final: 0.8833 (tpp) REVERT: E 328 LEU cc_start: 0.9511 (mt) cc_final: 0.9236 (mp) REVERT: E 567 ASN cc_start: 0.8958 (m-40) cc_final: 0.8603 (t0) REVERT: E 625 THR cc_start: 0.7026 (m) cc_final: 0.6814 (p) REVERT: E 1055 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8125 (pm20) REVERT: E 1108 MET cc_start: 0.8444 (tpt) cc_final: 0.7963 (tpt) REVERT: E 1150 TRP cc_start: 0.6553 (m100) cc_final: 0.6071 (m100) REVERT: E 1205 MET cc_start: 0.6573 (mtt) cc_final: 0.5767 (ttm) REVERT: E 1285 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8648 (tm-30) REVERT: I 144 MET cc_start: 0.7493 (mtt) cc_final: 0.7249 (mtt) REVERT: I 194 MET cc_start: 0.9533 (tpp) cc_final: 0.9143 (tpt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1830 time to fit residues: 107.4909 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 : 1.069 ------------------------------------------------------------------------------- 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: 0.9990 chunk 353 optimal weight: 7.9990 chunk 382 optimal weight: 0.3980 chunk 380 optimal weight: 0.0570 chunk 168 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 131 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 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 = 0.3889 r_free = 0.3889 target = 0.082885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061791 restraints weight = 177433.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063424 restraints weight = 95782.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064646 restraints weight = 64347.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065178 restraints weight = 46903.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.065645 restraints weight = 39453.698| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31566 Z= 0.109 Angle : 0.559 9.558 42806 Z= 0.280 Chirality : 0.040 0.232 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.198 52.113 4235 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.88 (0.14), residues: 3768 helix: 1.70 (0.11), residues: 2220 sheet: -1.60 (0.25), residues: 386 loop : -0.74 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 616 TYR 0.015 0.001 TYR A1880 PHE 0.031 0.001 PHE A1103 TRP 0.077 0.001 TRP A1269 HIS 0.007 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00234 (31566) covalent geometry : angle 0.55921 (42806) hydrogen bonds : bond 0.03552 ( 1714) hydrogen bonds : angle 4.15927 ( 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 361 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.075 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 311 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8242 (tpp80) REVERT: A 733 MET cc_start: 0.9357 (mmm) cc_final: 0.8904 (mmp) REVERT: A 756 MET cc_start: 0.7452 (mmt) cc_final: 0.7120 (mmm) REVERT: A 883 GLU cc_start: 0.8923 (mm-30) cc_final: 0.7920 (tp30) REVERT: A 956 MET cc_start: 0.9257 (tpp) cc_final: 0.8807 (tpp) REVERT: A 994 MET cc_start: 0.9190 (tpp) cc_final: 0.8675 (tpp) REVERT: A 1031 MET cc_start: 0.9172 (tpp) cc_final: 0.8713 (tpp) REVERT: A 1033 GLU cc_start: 0.9155 (mp0) cc_final: 0.8866 (mp0) REVERT: A 1078 MET cc_start: 0.9265 (pmm) cc_final: 0.9048 (pmm) REVERT: A 1452 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8856 (pttm) REVERT: A 1512 MET cc_start: 0.8617 (ppp) cc_final: 0.8172 (ppp) REVERT: A 1598 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8044 (mm-30) REVERT: A 1633 TRP cc_start: 0.9163 (m100) cc_final: 0.8898 (m100) REVERT: A 1634 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8846 (tm-30) REVERT: A 1650 MET cc_start: 0.7971 (mmt) cc_final: 0.7708 (mmm) REVERT: A 1717 MET cc_start: 0.9230 (tpt) cc_final: 0.8966 (tpt) REVERT: A 1719 HIS cc_start: 0.8968 (m-70) cc_final: 0.8517 (m-70) REVERT: A 1724 MET cc_start: 0.8705 (mtm) cc_final: 0.8403 (mtp) REVERT: A 1747 MET cc_start: 0.9167 (ttm) cc_final: 0.8951 (ttt) REVERT: A 1761 LEU cc_start: 0.9207 (mt) cc_final: 0.8912 (mt) REVERT: A 1804 TYR cc_start: 0.7666 (m-80) cc_final: 0.7392 (m-80) REVERT: A 2014 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8776 (tm-30) REVERT: A 2026 MET cc_start: 0.9440 (mtp) cc_final: 0.9042 (mtt) REVERT: A 2029 GLU cc_start: 0.9135 (pt0) cc_final: 0.8854 (pp20) REVERT: A 2199 MET cc_start: 0.8854 (tpp) cc_final: 0.8474 (tpp) REVERT: A 2220 LEU cc_start: 0.9566 (mt) cc_final: 0.9366 (mt) REVERT: A 2303 LEU cc_start: 0.9571 (mt) cc_final: 0.9356 (mt) REVERT: A 2327 MET cc_start: 0.8987 (tpp) cc_final: 0.8128 (tmm) REVERT: A 2357 ASP cc_start: 0.8083 (t0) cc_final: 0.7816 (t0) REVERT: A 2366 MET cc_start: 0.8683 (mmt) cc_final: 0.8454 (mmm) REVERT: A 2382 MET cc_start: 0.8990 (mmm) cc_final: 0.8771 (mmt) REVERT: A 2506 ASP cc_start: 0.8794 (t0) cc_final: 0.8553 (t0) REVERT: A 2526 GLU cc_start: 0.9410 (tp30) cc_final: 0.8851 (tp30) REVERT: C 100 MET cc_start: 0.8301 (ppp) cc_final: 0.7854 (ppp) REVERT: C 273 MET cc_start: 0.7613 (ppp) cc_final: 0.7333 (ppp) REVERT: E 55 MET cc_start: 0.6205 (mmm) cc_final: 0.5435 (mmm) REVERT: E 71 ASP cc_start: 0.9136 (p0) cc_final: 0.8864 (p0) REVERT: E 192 PHE cc_start: 0.8293 (m-80) cc_final: 0.7729 (m-80) REVERT: E 207 LYS cc_start: 0.9829 (mtmt) cc_final: 0.9583 (mtmm) REVERT: E 328 LEU cc_start: 0.9502 (mt) cc_final: 0.9231 (mp) REVERT: E 422 MET cc_start: 0.6397 (ptt) cc_final: 0.5824 (tmm) REVERT: E 567 ASN cc_start: 0.8936 (m-40) cc_final: 0.8569 (t0) REVERT: E 625 THR cc_start: 0.7624 (m) cc_final: 0.7229 (p) REVERT: E 1055 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8195 (pm20) REVERT: E 1108 MET cc_start: 0.8475 (tpt) cc_final: 0.8028 (tpt) REVERT: E 1150 TRP cc_start: 0.6410 (m100) cc_final: 0.6047 (m100) REVERT: E 1205 MET cc_start: 0.6541 (mtt) cc_final: 0.5541 (ptm) REVERT: E 1243 MET cc_start: 0.5463 (ttt) cc_final: 0.5214 (ttt) REVERT: E 1285 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8616 (tm-30) REVERT: I 144 MET cc_start: 0.7493 (mtt) cc_final: 0.7254 (mtt) REVERT: I 194 MET cc_start: 0.9515 (tpp) cc_final: 0.9153 (tpt) REVERT: I 366 MET cc_start: 0.7189 (mpp) cc_final: 0.6919 (mpp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1789 time to fit residues: 107.8541 Evaluate side-chains 283 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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: 0.8980 chunk 196 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 281 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.082416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061567 restraints weight = 178245.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063083 restraints weight = 97082.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064055 restraints weight = 63192.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.064863 restraints weight = 47209.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065231 restraints weight = 37853.476| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31566 Z= 0.121 Angle : 0.576 11.506 42806 Z= 0.289 Chirality : 0.040 0.221 4846 Planarity : 0.004 0.065 5459 Dihedral : 4.237 53.136 4235 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 0.91 (0.14), residues: 3768 helix: 1.70 (0.11), residues: 2220 sheet: -1.53 (0.25), residues: 384 loop : -0.70 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 227 TYR 0.018 0.001 TYR A2332 PHE 0.034 0.001 PHE A1103 TRP 0.077 0.001 TRP A1269 HIS 0.007 0.001 HIS A2401 Details of bonding type rmsd covalent geometry : bond 0.00264 (31566) covalent geometry : angle 0.57640 (42806) hydrogen bonds : bond 0.03527 ( 1714) hydrogen bonds : angle 4.19313 ( 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 353 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.177 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: A 311 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8248 (tpp80) REVERT: A 733 MET cc_start: 0.9393 (mmm) cc_final: 0.8979 (mmm) REVERT: A 756 MET cc_start: 0.7457 (mmt) cc_final: 0.7115 (mmm) REVERT: A 813 MET cc_start: 0.8564 (ppp) cc_final: 0.7900 (ppp) REVERT: A 883 GLU cc_start: 0.8937 (mm-30) cc_final: 0.7926 (tp30) REVERT: A 956 MET cc_start: 0.9296 (tpp) cc_final: 0.8845 (tpp) REVERT: A 994 MET cc_start: 0.9245 (tpp) cc_final: 0.8668 (tpp) REVERT: A 1031 MET cc_start: 0.9191 (tpp) cc_final: 0.8637 (tpp) REVERT: A 1033 GLU cc_start: 0.9168 (mp0) cc_final: 0.8888 (mp0) REVERT: A 1199 LEU cc_start: 0.9192 (mt) cc_final: 0.8899 (mt) REVERT: A 1452 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8827 (pttm) REVERT: A 1512 MET cc_start: 0.8666 (ppp) cc_final: 0.8248 (ppp) REVERT: A 1529 MET cc_start: 0.9344 (mtp) cc_final: 0.8862 (mmm) REVERT: A 1598 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 1633 TRP cc_start: 0.9138 (m100) cc_final: 0.8829 (m100) REVERT: A 1634 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8878 (tm-30) REVERT: A 1650 MET cc_start: 0.8035 (mmt) cc_final: 0.7793 (mmm) REVERT: A 1717 MET cc_start: 0.9323 (tpt) cc_final: 0.8831 (tpp) REVERT: A 1719 HIS cc_start: 0.9017 (m-70) cc_final: 0.8545 (m-70) REVERT: A 1724 MET cc_start: 0.8780 (mtm) cc_final: 0.8483 (mtp) REVERT: A 1761 LEU cc_start: 0.9231 (mt) cc_final: 0.8911 (mt) REVERT: A 1804 TYR cc_start: 0.7720 (m-80) cc_final: 0.7462 (m-80) REVERT: A 2014 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8828 (tm-30) REVERT: A 2026 MET cc_start: 0.9434 (mtp) cc_final: 0.9056 (mtt) REVERT: A 2029 GLU cc_start: 0.9182 (pt0) cc_final: 0.8907 (pp20) REVERT: A 2199 MET cc_start: 0.8970 (tpp) cc_final: 0.8558 (tpp) REVERT: A 2220 LEU cc_start: 0.9557 (mt) cc_final: 0.9347 (mt) REVERT: A 2303 LEU cc_start: 0.9581 (mt) cc_final: 0.9363 (mt) REVERT: A 2357 ASP cc_start: 0.8112 (t0) cc_final: 0.7848 (t0) REVERT: A 2366 MET cc_start: 0.8718 (mmt) cc_final: 0.8407 (mmm) REVERT: A 2382 MET cc_start: 0.9029 (mmm) cc_final: 0.8797 (mmt) REVERT: A 2506 ASP cc_start: 0.8863 (t0) cc_final: 0.8609 (t0) REVERT: A 2526 GLU cc_start: 0.9441 (tp30) cc_final: 0.8908 (tp30) REVERT: C 67 MET cc_start: 0.8696 (mtp) cc_final: 0.8476 (mtp) REVERT: C 100 MET cc_start: 0.8401 (ppp) cc_final: 0.7782 (ppp) REVERT: C 157 LEU cc_start: 0.8426 (tt) cc_final: 0.8025 (mt) REVERT: C 273 MET cc_start: 0.7632 (ppp) cc_final: 0.7379 (ppp) REVERT: E 55 MET cc_start: 0.6094 (mmm) cc_final: 0.5376 (mmm) REVERT: E 71 ASP cc_start: 0.9205 (p0) cc_final: 0.8933 (p0) REVERT: E 192 PHE cc_start: 0.8362 (m-80) cc_final: 0.7684 (m-80) REVERT: E 207 LYS cc_start: 0.9833 (mtmt) cc_final: 0.9582 (mtmm) REVERT: E 321 ASP cc_start: 0.9308 (m-30) cc_final: 0.8846 (p0) REVERT: E 328 LEU cc_start: 0.9502 (mt) cc_final: 0.9230 (mp) REVERT: E 567 ASN cc_start: 0.8923 (m-40) cc_final: 0.8573 (t0) REVERT: E 615 VAL cc_start: 0.9102 (t) cc_final: 0.8764 (p) REVERT: E 625 THR cc_start: 0.7451 (m) cc_final: 0.7079 (p) REVERT: E 1055 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8326 (pm20) REVERT: E 1105 ASN cc_start: 0.9620 (m-40) cc_final: 0.9233 (p0) REVERT: E 1108 MET cc_start: 0.8444 (tpt) cc_final: 0.7616 (tpt) REVERT: E 1150 TRP cc_start: 0.6564 (m100) cc_final: 0.6157 (m100) REVERT: E 1205 MET cc_start: 0.6548 (mtt) cc_final: 0.5516 (ptm) REVERT: E 1243 MET cc_start: 0.5336 (ttt) cc_final: 0.5110 (ttt) REVERT: E 1285 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8645 (tm-30) REVERT: I 144 MET cc_start: 0.7581 (mtt) cc_final: 0.7357 (mtt) REVERT: I 166 MET cc_start: 0.8848 (mmp) cc_final: 0.8445 (tpp) REVERT: I 194 MET cc_start: 0.9543 (tpp) cc_final: 0.9113 (tpt) REVERT: I 366 MET cc_start: 0.7165 (mpp) cc_final: 0.6824 (mpp) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1795 time to fit residues: 105.9676 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 : 1.127 ------------------------------------------------------------------------------- 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: 5.9990 chunk 355 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 289 optimal weight: 0.0970 chunk 240 optimal weight: 0.6980 chunk 246 optimal weight: 3.9990 chunk 291 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 281 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 650 GLN ** E1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.082525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.061495 restraints weight = 178630.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.063192 restraints weight = 96660.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064111 restraints weight = 63228.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.064925 restraints weight = 47559.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.065408 restraints weight = 38427.737| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31566 Z= 0.118 Angle : 0.574 10.175 42806 Z= 0.287 Chirality : 0.040 0.220 4846 Planarity : 0.004 0.066 5459 Dihedral : 4.207 54.299 4235 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3768 helix: 1.68 (0.11), residues: 2229 sheet: -1.56 (0.25), residues: 384 loop : -0.66 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 616 TYR 0.016 0.001 TYR A2332 PHE 0.031 0.001 PHE I 114 TRP 0.082 0.001 TRP A1269 HIS 0.004 0.001 HIS A2355 Details of bonding type rmsd covalent geometry : bond 0.00259 (31566) covalent geometry : angle 0.57384 (42806) hydrogen bonds : bond 0.03467 ( 1714) hydrogen bonds : angle 4.18280 ( 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 335 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.181 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: A 311 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8237 (tpp80) REVERT: A 733 MET cc_start: 0.9360 (mmm) cc_final: 0.8940 (mmm) REVERT: A 756 MET cc_start: 0.7406 (mmt) cc_final: 0.7079 (mmm) REVERT: A 813 MET cc_start: 0.8520 (ppp) cc_final: 0.7842 (ppp) REVERT: A 883 GLU cc_start: 0.8938 (mm-30) cc_final: 0.7937 (tp30) REVERT: A 956 MET cc_start: 0.9237 (tpp) cc_final: 0.8835 (tpp) REVERT: A 994 MET cc_start: 0.9191 (tpp) cc_final: 0.8656 (tpp) REVERT: A 1031 MET cc_start: 0.9081 (tpp) cc_final: 0.8601 (tpp) REVERT: A 1033 GLU cc_start: 0.9127 (mp0) cc_final: 0.8885 (mp0) REVERT: A 1038 MET cc_start: 0.8946 (tpp) cc_final: 0.8704 (tpp) REVERT: A 1199 LEU cc_start: 0.9147 (mt) cc_final: 0.8943 (mt) REVERT: A 1313 MET cc_start: 0.8323 (mmp) cc_final: 0.8036 (mmp) REVERT: A 1452 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8817 (pttm) REVERT: A 1477 MET cc_start: 0.9365 (tpt) cc_final: 0.8494 (tpt) REVERT: A 1512 MET cc_start: 0.8641 (ppp) cc_final: 0.8178 (ppp) REVERT: A 1529 MET cc_start: 0.9337 (mtp) cc_final: 0.8942 (mmm) REVERT: A 1535 MET cc_start: 0.8615 (tpt) cc_final: 0.8380 (ptp) REVERT: A 1598 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 1633 TRP cc_start: 0.9153 (m100) cc_final: 0.8866 (m100) REVERT: A 1634 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8858 (tm-30) REVERT: A 1719 HIS cc_start: 0.8969 (m-70) cc_final: 0.8526 (m-70) REVERT: A 1724 MET cc_start: 0.8791 (mtm) cc_final: 0.8468 (mtp) REVERT: A 1761 LEU cc_start: 0.9246 (mt) cc_final: 0.8936 (mt) REVERT: A 1804 TYR cc_start: 0.7648 (m-80) cc_final: 0.7384 (m-10) REVERT: A 2010 MET cc_start: 0.9005 (mmt) cc_final: 0.8580 (mmt) REVERT: A 2011 MET cc_start: 0.9470 (tmm) cc_final: 0.9149 (tmm) REVERT: A 2026 MET cc_start: 0.9446 (mtp) cc_final: 0.9060 (mtt) REVERT: A 2029 GLU cc_start: 0.9144 (pt0) cc_final: 0.8876 (pp20) REVERT: A 2195 ASP cc_start: 0.9127 (m-30) cc_final: 0.8826 (m-30) REVERT: A 2199 MET cc_start: 0.8965 (tpp) cc_final: 0.8540 (tpp) REVERT: A 2303 LEU cc_start: 0.9573 (mt) cc_final: 0.9347 (mt) REVERT: A 2327 MET cc_start: 0.9015 (tpp) cc_final: 0.8261 (tmm) REVERT: A 2345 MET cc_start: 0.8777 (mtp) cc_final: 0.8286 (mtm) REVERT: A 2357 ASP cc_start: 0.8009 (t0) cc_final: 0.7699 (t0) REVERT: A 2366 MET cc_start: 0.8719 (mmt) cc_final: 0.8394 (mmm) REVERT: A 2382 MET cc_start: 0.9007 (mmm) cc_final: 0.8784 (mmt) REVERT: A 2506 ASP cc_start: 0.8803 (t0) cc_final: 0.8580 (t0) REVERT: A 2526 GLU cc_start: 0.9409 (tp30) cc_final: 0.8989 (tp30) REVERT: C 67 MET cc_start: 0.8653 (mtp) cc_final: 0.8452 (mtp) REVERT: C 100 MET cc_start: 0.8364 (ppp) cc_final: 0.7750 (ppp) REVERT: C 157 LEU cc_start: 0.8346 (tt) cc_final: 0.7979 (mt) REVERT: C 273 MET cc_start: 0.7584 (ppp) cc_final: 0.7329 (ppp) REVERT: E 51 MET cc_start: 0.8110 (tpp) cc_final: 0.7460 (tpp) REVERT: E 55 MET cc_start: 0.6138 (mmm) cc_final: 0.5415 (mmm) REVERT: E 71 ASP cc_start: 0.9173 (p0) cc_final: 0.8904 (p0) REVERT: E 328 LEU cc_start: 0.9520 (mt) cc_final: 0.9249 (mp) REVERT: E 567 ASN cc_start: 0.8922 (m-40) cc_final: 0.8578 (t0) REVERT: E 615 VAL cc_start: 0.9139 (t) cc_final: 0.8810 (p) REVERT: E 625 THR cc_start: 0.7426 (m) cc_final: 0.7054 (p) REVERT: E 1105 ASN cc_start: 0.9631 (m-40) cc_final: 0.9250 (p0) REVERT: E 1108 MET cc_start: 0.8510 (tpt) cc_final: 0.7761 (tpt) REVERT: E 1150 TRP cc_start: 0.6725 (m100) cc_final: 0.6160 (m100) REVERT: E 1195 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7539 (ptp-170) REVERT: E 1205 MET cc_start: 0.6574 (mtt) cc_final: 0.5565 (ptm) REVERT: E 1285 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8599 (tm-30) REVERT: I 166 MET cc_start: 0.8795 (mmp) cc_final: 0.8363 (tpp) REVERT: I 194 MET cc_start: 0.9515 (tpp) cc_final: 0.9118 (tpt) REVERT: I 366 MET cc_start: 0.7125 (mpp) cc_final: 0.6804 (mpp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1808 time to fit residues: 100.6740 Evaluate side-chains 273 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 0.9980 chunk 337 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 346 optimal weight: 0.0020 chunk 356 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 330 optimal weight: 0.0770 chunk 193 optimal weight: 0.7980 chunk 325 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3888 r_free = 0.3888 target = 0.082954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062038 restraints weight = 178754.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063533 restraints weight = 98541.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064571 restraints weight = 63148.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.065291 restraints weight = 47267.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065870 restraints weight = 38353.340| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4926 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 : 0.576 9.833 42806 Z= 0.287 Chirality : 0.040 0.267 4846 Planarity : 0.004 0.112 5459 Dihedral : 4.224 55.201 4235 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.93 (0.14), residues: 3768 helix: 1.67 (0.11), residues: 2230 sheet: -1.47 (0.25), residues: 387 loop : -0.65 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 616 TYR 0.014 0.001 TYR E1324 PHE 0.028 0.001 PHE A1103 TRP 0.031 0.001 TRP C 272 HIS 0.008 0.001 HIS A1988 Details of bonding type rmsd covalent geometry : bond 0.00241 (31566) covalent geometry : angle 0.57617 (42806) hydrogen bonds : bond 0.03422 ( 1714) hydrogen bonds : angle 4.12848 ( 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 342 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.160 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 311 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8233 (tpp80) REVERT: A 484 THR cc_start: 0.4764 (m) cc_final: 0.4557 (p) REVERT: A 733 MET cc_start: 0.9351 (mmm) cc_final: 0.8905 (mmp) REVERT: A 756 MET cc_start: 0.7483 (mmt) cc_final: 0.7141 (mmm) REVERT: A 813 MET cc_start: 0.8582 (ppp) cc_final: 0.7953 (ppp) REVERT: A 883 GLU cc_start: 0.8899 (mm-30) cc_final: 0.7876 (tp30) REVERT: A 956 MET cc_start: 0.9201 (tpp) cc_final: 0.8778 (tpp) REVERT: A 994 MET cc_start: 0.9170 (tpp) cc_final: 0.8644 (tpp) REVERT: A 1031 MET cc_start: 0.9090 (tpp) cc_final: 0.8602 (tpp) REVERT: A 1033 GLU cc_start: 0.9118 (mp0) cc_final: 0.8877 (mp0) REVERT: A 1199 LEU cc_start: 0.9177 (mt) cc_final: 0.8950 (mt) REVERT: A 1313 MET cc_start: 0.8360 (mmp) cc_final: 0.7785 (mmt) REVERT: A 1452 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8802 (pttm) REVERT: A 1477 MET cc_start: 0.9302 (tpt) cc_final: 0.8498 (tpp) REVERT: A 1512 MET cc_start: 0.8666 (ppp) cc_final: 0.8204 (ppp) REVERT: A 1529 MET cc_start: 0.9348 (mtp) cc_final: 0.8980 (mmm) REVERT: A 1598 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 1633 TRP cc_start: 0.9137 (m100) cc_final: 0.8786 (m100) REVERT: A 1634 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8850 (tm-30) REVERT: A 1638 MET cc_start: 0.8240 (tpt) cc_final: 0.7906 (tpp) REVERT: A 1650 MET cc_start: 0.8412 (mmp) cc_final: 0.8013 (mmp) REVERT: A 1719 HIS cc_start: 0.8955 (m-70) cc_final: 0.8500 (m-70) REVERT: A 1724 MET cc_start: 0.8783 (mtm) cc_final: 0.8499 (mtp) REVERT: A 1761 LEU cc_start: 0.9237 (mt) cc_final: 0.8952 (mt) REVERT: A 2026 MET cc_start: 0.9437 (mtp) cc_final: 0.9056 (mtt) REVERT: A 2029 GLU cc_start: 0.9128 (pt0) cc_final: 0.8859 (pp20) REVERT: A 2195 ASP cc_start: 0.9107 (m-30) cc_final: 0.8816 (m-30) REVERT: A 2199 MET cc_start: 0.8954 (tpp) cc_final: 0.8527 (tpp) REVERT: A 2303 LEU cc_start: 0.9558 (mt) cc_final: 0.9348 (mt) REVERT: A 2345 MET cc_start: 0.8762 (mtp) cc_final: 0.8275 (mtm) REVERT: A 2357 ASP cc_start: 0.7929 (t0) cc_final: 0.7520 (t0) REVERT: A 2366 MET cc_start: 0.8678 (mmt) cc_final: 0.8407 (mmm) REVERT: A 2382 MET cc_start: 0.9001 (mmm) cc_final: 0.8775 (mmt) REVERT: A 2506 ASP cc_start: 0.8784 (t0) cc_final: 0.8545 (t0) REVERT: A 2526 GLU cc_start: 0.9393 (tp30) cc_final: 0.8961 (tp30) REVERT: C 100 MET cc_start: 0.8325 (ppp) cc_final: 0.7715 (ppp) REVERT: C 157 LEU cc_start: 0.8362 (tt) cc_final: 0.8016 (mt) REVERT: E 51 MET cc_start: 0.8034 (tpp) cc_final: 0.7396 (tpp) REVERT: E 55 MET cc_start: 0.6133 (mmm) cc_final: 0.5404 (mmm) REVERT: E 71 ASP cc_start: 0.9152 (p0) cc_final: 0.8886 (p0) REVERT: E 321 ASP cc_start: 0.9227 (m-30) cc_final: 0.8646 (p0) REVERT: E 328 LEU cc_start: 0.9504 (mt) cc_final: 0.9238 (mp) REVERT: E 567 ASN cc_start: 0.8895 (m-40) cc_final: 0.8547 (t0) REVERT: E 615 VAL cc_start: 0.9111 (t) cc_final: 0.8771 (p) REVERT: E 625 THR cc_start: 0.7389 (m) cc_final: 0.7019 (p) REVERT: E 1049 TRP cc_start: 0.8031 (m100) cc_final: 0.7795 (t-100) REVERT: E 1105 ASN cc_start: 0.9620 (m-40) cc_final: 0.9233 (p0) REVERT: E 1108 MET cc_start: 0.8425 (tpt) cc_final: 0.7623 (tpt) REVERT: E 1150 TRP cc_start: 0.6722 (m100) cc_final: 0.6340 (m100) REVERT: E 1205 MET cc_start: 0.6673 (mtt) cc_final: 0.5597 (ptm) REVERT: E 1243 MET cc_start: 0.5430 (ttt) cc_final: 0.5229 (ttt) REVERT: E 1285 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8601 (tm-30) REVERT: E 1324 TYR cc_start: 0.7070 (m-80) cc_final: 0.6784 (m-80) REVERT: I 166 MET cc_start: 0.8795 (mmp) cc_final: 0.8369 (tpp) REVERT: I 194 MET cc_start: 0.9521 (tpp) cc_final: 0.9123 (tpt) REVERT: I 366 MET cc_start: 0.7029 (mpp) cc_final: 0.6820 (mpp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1775 time to fit residues: 100.8024 Evaluate side-chains 273 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 337 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 334 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 381 optimal weight: 0.2980 chunk 189 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3879 r_free = 0.3879 target = 0.082579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.061701 restraints weight = 180058.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063182 restraints weight = 99163.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.064297 restraints weight = 64722.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.064995 restraints weight = 47451.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.065584 restraints weight = 38245.396| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4992 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= 0.117 Angle : 0.582 9.580 42806 Z= 0.292 Chirality : 0.040 0.185 4846 Planarity : 0.004 0.088 5459 Dihedral : 4.221 56.503 4235 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.95 (0.14), residues: 3768 helix: 1.69 (0.11), residues: 2229 sheet: -1.41 (0.25), residues: 388 loop : -0.65 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 616 TYR 0.020 0.001 TYR A1656 PHE 0.027 0.001 PHE A1103 TRP 0.073 0.001 TRP A1269 HIS 0.008 0.001 HIS E 978 Details of bonding type rmsd covalent geometry : bond 0.00258 (31566) covalent geometry : angle 0.58225 (42806) hydrogen bonds : bond 0.03401 ( 1714) hydrogen bonds : angle 4.19958 ( 5019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5964.83 seconds wall clock time: 103 minutes 31.14 seconds (6211.14 seconds total)