Starting phenix.real_space_refine on Mon Jul 6 17:47:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.map" model { file = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oik_12931/07_2026/7oik_12931.cif" } resolution = 3.5 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 23443 2.51 5 N 6312 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36779 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 35505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4426, 35505 Classifications: {'peptide': 4426} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 183, 'TRANS': 4242} Chain breaks: 15 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 138} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26526 SG CYS A3962 89.136 133.575 219.167 1.00485.84 S ATOM 26690 SG CYS A3982 86.914 131.918 222.010 1.00504.02 S ATOM 26715 SG CYS A3985 90.759 132.082 222.071 1.00513.48 S ATOM 26416 SG CYS A3947 79.101 126.941 217.704 1.00394.59 S ATOM 26441 SG CYS A3950 76.880 123.812 216.785 1.00385.02 S ATOM 26569 SG CYS A3967 76.748 126.402 214.552 1.00428.91 S ATOM 26594 SG CYS A3970 75.336 127.264 217.955 1.00452.42 S Time building chain proxies: 7.31, per 1000 atoms: 0.20 Number of scatterers: 36779 At special positions: 0 Unit cell: (131.856, 154.368, 244.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 214 16.00 P 3 15.00 Mg 1 11.99 O 6804 8.00 N 6312 7.00 C 23443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 992 " distance=2.03 Simple disulfide: pdb=" SG CYS A2605 " - pdb=" SG CYS A2653 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" ND1 HIS A3964 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3985 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3962 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3982 " pdb=" ZN A5204 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3967 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3950 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3970 " pdb="ZN ZN A5204 " - pdb=" SG CYS A3947 " Number of angles added : 9 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8768 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 16 sheets defined 60.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 492 through 513 Processing helix chain 'A' and resid 517 through 535 removed outlier: 3.618A pdb=" N VAL A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 576 removed outlier: 3.716A pdb=" N TRP A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Proline residue: A 572 - end of helix removed outlier: 3.719A pdb=" N GLU A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.520A pdb=" N HIS A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 666 removed outlier: 4.131A pdb=" N LEU A 665 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.772A pdb=" N LEU A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 4.119A pdb=" N TRP A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 4.028A pdb=" N GLU A 702 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 removed outlier: 4.171A pdb=" N GLN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 720 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 4.549A pdb=" N ARG A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.648A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 775 removed outlier: 3.879A pdb=" N ASP A 763 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Proline residue: A 773 - end of helix Processing helix chain 'A' and resid 780 through 800 removed outlier: 3.918A pdb=" N LYS A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 827 Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.934A pdb=" N ILE A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 Processing helix chain 'A' and resid 908 through 917 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.537A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 982 Processing helix chain 'A' and resid 994 through 1010 removed outlier: 3.562A pdb=" N PHE A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1032 through 1044 removed outlier: 4.010A pdb=" N GLN A1036 " --> pdb=" O PRO A1032 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1072 removed outlier: 3.914A pdb=" N GLN A1057 " --> pdb=" O GLU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1089 Processing helix chain 'A' and resid 1089 through 1101 Processing helix chain 'A' and resid 1113 through 1143 Processing helix chain 'A' and resid 1154 through 1159 Processing helix chain 'A' and resid 1166 through 1171 removed outlier: 3.577A pdb=" N ASN A1169 " --> pdb=" O LYS A1166 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A1171 " --> pdb=" O LEU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1233 through 1241 removed outlier: 3.811A pdb=" N LEU A1238 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A1239 " --> pdb=" O PRO A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.987A pdb=" N CYS A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1271 through 1274 removed outlier: 4.079A pdb=" N VAL A1274 " --> pdb=" O LYS A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1271 through 1274' Processing helix chain 'A' and resid 1277 through 1289 Processing helix chain 'A' and resid 1298 through 1329 removed outlier: 4.008A pdb=" N ARG A1302 " --> pdb=" O TRP A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1346 removed outlier: 3.574A pdb=" N ASP A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1377 through 1387 Processing helix chain 'A' and resid 1388 through 1398 Processing helix chain 'A' and resid 1403 through 1415 removed outlier: 4.139A pdb=" N ASP A1409 " --> pdb=" O LYS A1405 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A1413 " --> pdb=" O ASP A1409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1440 removed outlier: 4.488A pdb=" N VAL A1425 " --> pdb=" O ASP A1421 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER A1437 " --> pdb=" O GLN A1433 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A1438 " --> pdb=" O GLY A1434 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A1440 " --> pdb=" O ALA A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1464 removed outlier: 3.814A pdb=" N GLU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A1464 " --> pdb=" O ARG A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1478 through 1487 removed outlier: 4.264A pdb=" N LYS A1486 " --> pdb=" O LEU A1482 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A1487 " --> pdb=" O LYS A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1507 removed outlier: 3.717A pdb=" N ALA A1500 " --> pdb=" O SER A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1557 Processing helix chain 'A' and resid 1563 through 1594 removed outlier: 3.560A pdb=" N ASN A1567 " --> pdb=" O ASP A1563 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A1594 " --> pdb=" O LEU A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1660 removed outlier: 3.652A pdb=" N GLU A1659 " --> pdb=" O GLN A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1666 Processing helix chain 'A' and resid 1667 through 1679 removed outlier: 4.348A pdb=" N ARG A1679 " --> pdb=" O SER A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'A' and resid 1692 through 1694 No H-bonds generated for 'chain 'A' and resid 1692 through 1694' Processing helix chain 'A' and resid 1699 through 1709 Processing helix chain 'A' and resid 1713 through 1726 removed outlier: 3.562A pdb=" N TYR A1717 " --> pdb=" O LYS A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.518A pdb=" N LEU A1731 " --> pdb=" O PRO A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 3.908A pdb=" N LYS A1739 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1754 Processing helix chain 'A' and resid 1760 through 1775 removed outlier: 3.793A pdb=" N GLY A1775 " --> pdb=" O LEU A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1801 Processing helix chain 'A' and resid 1802 through 1810 removed outlier: 3.745A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1844 removed outlier: 4.063A pdb=" N VAL A1836 " --> pdb=" O THR A1832 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1862 removed outlier: 3.852A pdb=" N LEU A1862 " --> pdb=" O ALA A1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1859 through 1862' Processing helix chain 'A' and resid 1863 through 1881 removed outlier: 3.779A pdb=" N ALA A1881 " --> pdb=" O LEU A1877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1905 Processing helix chain 'A' and resid 1906 through 1909 Processing helix chain 'A' and resid 1917 through 1930 Processing helix chain 'A' and resid 1937 through 1942 removed outlier: 3.950A pdb=" N THR A1940 " --> pdb=" O SER A1937 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A1941 " --> pdb=" O ALA A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1959 through 1974 Processing helix chain 'A' and resid 1993 through 2002 removed outlier: 3.996A pdb=" N VAL A1997 " --> pdb=" O ASP A1993 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2037 removed outlier: 3.605A pdb=" N PHE A2031 " --> pdb=" O GLY A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2085 Processing helix chain 'A' and resid 2086 through 2088 No H-bonds generated for 'chain 'A' and resid 2086 through 2088' Processing helix chain 'A' and resid 2116 through 2121 Processing helix chain 'A' and resid 2122 through 2137 Proline residue: A2128 - end of helix removed outlier: 4.090A pdb=" N ARG A2134 " --> pdb=" O GLN A2130 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A2137 " --> pdb=" O LYS A2133 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2166 Processing helix chain 'A' and resid 2172 through 2193 removed outlier: 3.558A pdb=" N LEU A2176 " --> pdb=" O SER A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2203 Processing helix chain 'A' and resid 2207 through 2224 removed outlier: 4.058A pdb=" N PHE A2211 " --> pdb=" O GLY A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2250 through 2255 removed outlier: 3.913A pdb=" N LEU A2255 " --> pdb=" O ALA A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2318 Processing helix chain 'A' and resid 2330 through 2342 Processing helix chain 'A' and resid 2357 through 2374 Processing helix chain 'A' and resid 2387 through 2400 Processing helix chain 'A' and resid 2417 through 2440 removed outlier: 3.697A pdb=" N ILE A2421 " --> pdb=" O THR A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2464 Processing helix chain 'A' and resid 2492 through 2501 removed outlier: 3.603A pdb=" N ILE A2496 " --> pdb=" O SER A2492 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2525 Processing helix chain 'A' and resid 2550 through 2564 removed outlier: 4.428A pdb=" N ASP A2564 " --> pdb=" O GLN A2560 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2568 removed outlier: 4.156A pdb=" N VAL A2568 " --> pdb=" O SER A2565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2565 through 2568' Processing helix chain 'A' and resid 2571 through 2589 Processing helix chain 'A' and resid 2600 through 2615 Processing helix chain 'A' and resid 2617 through 2631 removed outlier: 3.727A pdb=" N LYS A2621 " --> pdb=" O ASP A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2642 through 2654 removed outlier: 3.527A pdb=" N TYR A2654 " --> pdb=" O ILE A2650 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2669 Processing helix chain 'A' and resid 2673 through 2677 removed outlier: 3.717A pdb=" N ASN A2677 " --> pdb=" O LYS A2674 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.859A pdb=" N ILE A2682 " --> pdb=" O SER A2678 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A2697 " --> pdb=" O PHE A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2706 through 2722 Processing helix chain 'A' and resid 2737 through 2747 Processing helix chain 'A' and resid 2775 through 2791 removed outlier: 3.993A pdb=" N ILE A2779 " --> pdb=" O THR A2775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2817 through 2819 No H-bonds generated for 'chain 'A' and resid 2817 through 2819' Processing helix chain 'A' and resid 2820 through 2825 removed outlier: 3.562A pdb=" N LEU A2824 " --> pdb=" O THR A2820 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2880 Processing helix chain 'A' and resid 2883 through 2889 Processing helix chain 'A' and resid 2892 through 2907 Processing helix chain 'A' and resid 2913 through 2932 removed outlier: 3.600A pdb=" N TYR A2917 " --> pdb=" O GLY A2913 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A2932 " --> pdb=" O ALA A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2948 Processing helix chain 'A' and resid 2955 through 2961 Processing helix chain 'A' and resid 2974 through 2984 removed outlier: 3.671A pdb=" N LEU A2978 " --> pdb=" O SER A2974 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3018 removed outlier: 3.940A pdb=" N ILE A3014 " --> pdb=" O VAL A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3056 Processing helix chain 'A' and resid 3071 through 3077 removed outlier: 3.713A pdb=" N GLN A3077 " --> pdb=" O ASP A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3113 through 3120 removed outlier: 3.880A pdb=" N PHE A3120 " --> pdb=" O VAL A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3128 removed outlier: 3.681A pdb=" N LEU A3128 " --> pdb=" O ILE A3125 " (cutoff:3.500A) Processing helix chain 'A' and resid 3140 through 3159 Processing helix chain 'A' and resid 3172 through 3177 Processing helix chain 'A' and resid 3183 through 3197 removed outlier: 3.933A pdb=" N SER A3187 " --> pdb=" O ASP A3183 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A3197 " --> pdb=" O VAL A3193 " (cutoff:3.500A) Processing helix chain 'A' and resid 3204 through 3219 removed outlier: 4.048A pdb=" N LYS A3208 " --> pdb=" O GLU A3204 " (cutoff:3.500A) Processing helix chain 'A' and resid 3222 through 3229 Processing helix chain 'A' and resid 3230 through 3232 No H-bonds generated for 'chain 'A' and resid 3230 through 3232' Processing helix chain 'A' and resid 3236 through 3249 Processing helix chain 'A' and resid 3254 through 3263 Processing helix chain 'A' and resid 3287 through 3295 Processing helix chain 'A' and resid 3309 through 3311 No H-bonds generated for 'chain 'A' and resid 3309 through 3311' Processing helix chain 'A' and resid 3313 through 3326 removed outlier: 4.124A pdb=" N PHE A3317 " --> pdb=" O THR A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3348 through 3365 removed outlier: 4.446A pdb=" N SER A3352 " --> pdb=" O GLN A3348 " (cutoff:3.500A) Processing helix chain 'A' and resid 3413 through 3420 removed outlier: 3.631A pdb=" N LEU A3417 " --> pdb=" O ASP A3413 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A3420 " --> pdb=" O LYS A3416 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3426 removed outlier: 3.845A pdb=" N PHE A3426 " --> pdb=" O ILE A3422 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3490 removed outlier: 4.830A pdb=" N GLN A3486 " --> pdb=" O GLN A3482 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY A3487 " --> pdb=" O SER A3483 " (cutoff:3.500A) Processing helix chain 'A' and resid 3501 through 3512 Processing helix chain 'A' and resid 3517 through 3539 Processing helix chain 'A' and resid 3548 through 3555 Processing helix chain 'A' and resid 3556 through 3564 Processing helix chain 'A' and resid 3565 through 3590 Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3595 through 3600 Processing helix chain 'A' and resid 3604 through 3615 removed outlier: 3.882A pdb=" N GLN A3608 " --> pdb=" O PRO A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3676 removed outlier: 3.893A pdb=" N ILE A3661 " --> pdb=" O PHE A3657 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3691 Processing helix chain 'A' and resid 3692 through 3699 Processing helix chain 'A' and resid 3702 through 3722 Processing helix chain 'A' and resid 3727 through 3746 Processing helix chain 'A' and resid 3761 through 3784 removed outlier: 4.313A pdb=" N HIS A3765 " --> pdb=" O LEU A3761 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A3774 " --> pdb=" O HIS A3770 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A3778 " --> pdb=" O ARG A3774 " (cutoff:3.500A) Processing helix chain 'A' and resid 3787 through 3800 removed outlier: 3.919A pdb=" N SER A3791 " --> pdb=" O GLN A3787 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A3794 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A3796 " --> pdb=" O LEU A3792 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU A3797 " --> pdb=" O SER A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3807 through 3824 removed outlier: 3.945A pdb=" N ASP A3823 " --> pdb=" O MET A3819 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A3824 " --> pdb=" O LEU A3820 " (cutoff:3.500A) Processing helix chain 'A' and resid 3828 through 3839 removed outlier: 3.692A pdb=" N TRP A3832 " --> pdb=" O SER A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3839 through 3847 removed outlier: 3.516A pdb=" N CYS A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3856 through 3890 removed outlier: 5.313A pdb=" N LEU A3885 " --> pdb=" O GLU A3881 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY A3886 " --> pdb=" O HIS A3882 " (cutoff:3.500A) Processing helix chain 'A' and resid 3894 through 3910 removed outlier: 3.924A pdb=" N THR A3900 " --> pdb=" O PRO A3896 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER A3903 " --> pdb=" O THR A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3941 removed outlier: 3.875A pdb=" N PHE A3921 " --> pdb=" O THR A3917 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A3941 " --> pdb=" O LYS A3937 " (cutoff:3.500A) Processing helix chain 'A' and resid 3967 through 3975 Processing helix chain 'A' and resid 3999 through 4026 removed outlier: 4.241A pdb=" N LYS A4003 " --> pdb=" O GLN A3999 " (cutoff:3.500A) Processing helix chain 'A' and resid 4035 through 4045 removed outlier: 3.614A pdb=" N ILE A4039 " --> pdb=" O GLU A4035 " (cutoff:3.500A) Processing helix chain 'A' and resid 4082 through 4089 Processing helix chain 'A' and resid 4092 through 4095 removed outlier: 3.614A pdb=" N GLU A4095 " --> pdb=" O SER A4092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4092 through 4095' Processing helix chain 'A' and resid 4096 through 4111 removed outlier: 3.615A pdb=" N ILE A4100 " --> pdb=" O VAL A4096 " (cutoff:3.500A) Processing helix chain 'A' and resid 4116 through 4138 removed outlier: 4.233A pdb=" N LEU A4120 " --> pdb=" O ASP A4116 " (cutoff:3.500A) Processing helix chain 'A' and resid 4142 through 4156 removed outlier: 3.854A pdb=" N VAL A4146 " --> pdb=" O ASN A4142 " (cutoff:3.500A) Processing helix chain 'A' and resid 4171 through 4198 removed outlier: 3.634A pdb=" N GLU A4197 " --> pdb=" O SER A4193 " (cutoff:3.500A) Processing helix chain 'A' and resid 4204 through 4219 Processing helix chain 'A' and resid 4222 through 4236 Processing helix chain 'A' and resid 4237 through 4245 removed outlier: 3.911A pdb=" N VAL A4241 " --> pdb=" O GLY A4237 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4255 removed outlier: 3.503A pdb=" N VAL A4254 " --> pdb=" O CYS A4251 " (cutoff:3.500A) Processing helix chain 'A' and resid 4256 through 4262 removed outlier: 3.947A pdb=" N ILE A4260 " --> pdb=" O PRO A4256 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A4261 " --> pdb=" O ARG A4257 " (cutoff:3.500A) Processing helix chain 'A' and resid 4271 through 4276 removed outlier: 3.714A pdb=" N LEU A4274 " --> pdb=" O ASP A4271 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A4275 " --> pdb=" O ARG A4272 " (cutoff:3.500A) Processing helix chain 'A' and resid 4279 through 4293 removed outlier: 3.886A pdb=" N VAL A4283 " --> pdb=" O GLU A4279 " (cutoff:3.500A) Processing helix chain 'A' and resid 4296 through 4304 removed outlier: 4.031A pdb=" N GLY A4300 " --> pdb=" O THR A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4309 through 4331 removed outlier: 4.181A pdb=" N SER A4331 " --> pdb=" O ALA A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4342 through 4353 removed outlier: 3.529A pdb=" N VAL A4346 " --> pdb=" O GLN A4342 " (cutoff:3.500A) Processing helix chain 'A' and resid 4358 through 4370 removed outlier: 3.560A pdb=" N SER A4367 " --> pdb=" O CYS A4363 " (cutoff:3.500A) Processing helix chain 'A' and resid 4384 through 4403 removed outlier: 4.090A pdb=" N THR A4388 " --> pdb=" O ILE A4384 " (cutoff:3.500A) Processing helix chain 'A' and resid 4405 through 4407 No H-bonds generated for 'chain 'A' and resid 4405 through 4407' Processing helix chain 'A' and resid 4408 through 4417 Processing helix chain 'A' and resid 4418 through 4422 removed outlier: 3.773A pdb=" N ALA A4422 " --> pdb=" O VAL A4419 " (cutoff:3.500A) Processing helix chain 'A' and resid 4522 through 4544 removed outlier: 3.912A pdb=" N HIS A4543 " --> pdb=" O VAL A4539 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A4544 " --> pdb=" O GLY A4540 " (cutoff:3.500A) Processing helix chain 'A' and resid 4544 through 4552 removed outlier: 3.731A pdb=" N LEU A4548 " --> pdb=" O ASN A4544 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4581 through 4596 Processing helix chain 'A' and resid 4613 through 4633 Processing helix chain 'A' and resid 4638 through 4648 Processing helix chain 'A' and resid 4655 through 4660 removed outlier: 4.083A pdb=" N LYS A4659 " --> pdb=" O ASN A4655 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A4660 " --> pdb=" O PRO A4656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4655 through 4660' Processing helix chain 'A' and resid 4665 through 4669 removed outlier: 4.265A pdb=" N PHE A4668 " --> pdb=" O PRO A4665 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A4669 " --> pdb=" O ALA A4666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4665 through 4669' Processing helix chain 'A' and resid 4691 through 4702 Processing helix chain 'A' and resid 4708 through 4717 Processing helix chain 'A' and resid 4717 through 4722 Processing helix chain 'A' and resid 4723 through 4725 No H-bonds generated for 'chain 'A' and resid 4723 through 4725' Processing helix chain 'A' and resid 4726 through 4741 Processing helix chain 'A' and resid 4751 through 4757 Processing helix chain 'A' and resid 4761 through 4783 Processing helix chain 'A' and resid 4785 through 4790 Processing helix chain 'A' and resid 4820 through 4845 removed outlier: 3.868A pdb=" N THR A4824 " --> pdb=" O GLY A4820 " (cutoff:3.500A) Processing helix chain 'A' and resid 4859 through 4863 removed outlier: 3.794A pdb=" N HIS A4862 " --> pdb=" O ALA A4859 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A4863 " --> pdb=" O ASP A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4863' Processing helix chain 'A' and resid 4867 through 4872 Processing helix chain 'A' and resid 4872 through 4878 Processing helix chain 'A' and resid 4895 through 4905 Processing helix chain 'A' and resid 4930 through 4941 removed outlier: 3.543A pdb=" N PHE A4934 " --> pdb=" O TYR A4930 " (cutoff:3.500A) Processing helix chain 'A' and resid 4947 through 4957 removed outlier: 3.929A pdb=" N SER A4952 " --> pdb=" O ASN A4948 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A4957 " --> pdb=" O THR A4953 " (cutoff:3.500A) Processing helix chain 'A' and resid 4960 through 4980 removed outlier: 4.161A pdb=" N THR A4980 " --> pdb=" O GLY A4976 " (cutoff:3.500A) Processing helix chain 'A' and resid 4988 through 4994 removed outlier: 3.662A pdb=" N TYR A4992 " --> pdb=" O ASP A4988 " (cutoff:3.500A) Processing helix chain 'A' and resid 5003 through 5011 removed outlier: 3.893A pdb=" N LEU A5007 " --> pdb=" O THR A5003 " (cutoff:3.500A) Processing helix chain 'A' and resid 5012 through 5013 No H-bonds generated for 'chain 'A' and resid 5012 through 5013' Processing helix chain 'A' and resid 5014 through 5016 No H-bonds generated for 'chain 'A' and resid 5014 through 5016' Processing helix chain 'A' and resid 5017 through 5036 Processing helix chain 'A' and resid 5045 through 5049 Processing helix chain 'A' and resid 5053 through 5066 removed outlier: 4.112A pdb=" N GLU A5066 " --> pdb=" O THR A5062 " (cutoff:3.500A) Processing helix chain 'A' and resid 5068 through 5084 removed outlier: 4.339A pdb=" N LEU A5074 " --> pdb=" O ASP A5070 " (cutoff:3.500A) Processing helix chain 'A' and resid 5098 through 5107 Processing helix chain 'A' and resid 5115 through 5121 removed outlier: 3.755A pdb=" N GLN A5121 " --> pdb=" O GLU A5117 " (cutoff:3.500A) Processing helix chain 'A' and resid 5131 through 5149 removed outlier: 3.646A pdb=" N GLY A5149 " --> pdb=" O ARG A5145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 18 removed outlier: 3.583A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 100 through 114 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 1149 through 1150 removed outlier: 6.838A pdb=" N GLN A1149 " --> pdb=" O VAL A1232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1541 through 1544 removed outlier: 3.669A pdb=" N GLY A1612 " --> pdb=" O TYR A1606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1792 through 1796 removed outlier: 6.228A pdb=" N ASN A1793 " --> pdb=" O ILE A1890 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N CYS A1892 " --> pdb=" O ASN A1793 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A1795 " --> pdb=" O CYS A1892 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A1825 " --> pdb=" O LEU A1857 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1982 through 1987 removed outlier: 6.718A pdb=" N LYS A1983 " --> pdb=" O HIS A2017 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASP A2019 " --> pdb=" O LYS A1983 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A1985 " --> pdb=" O ASP A2019 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1951 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A2061 " --> pdb=" O VAL A1951 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A1953 " --> pdb=" O ILE A2061 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A2091 " --> pdb=" O VAL A1948 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A1950 " --> pdb=" O VAL A2091 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N CYS A2093 " --> pdb=" O ILE A1950 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A1952 " --> pdb=" O CYS A2093 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2040 through 2042 Processing sheet with id=AA6, first strand: chain 'A' and resid 2266 through 2269 Processing sheet with id=AA7, first strand: chain 'A' and resid 2282 through 2285 Processing sheet with id=AA8, first strand: chain 'A' and resid 2407 through 2411 removed outlier: 6.428A pdb=" N LYS A2408 " --> pdb=" O PHE A2446 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A2448 " --> pdb=" O LYS A2408 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A2410 " --> pdb=" O ASP A2448 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A2377 " --> pdb=" O ILE A2481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2467 through 2468 Processing sheet with id=AB1, first strand: chain 'A' and resid 2762 through 2768 removed outlier: 6.196A pdb=" N GLN A2762 " --> pdb=" O VAL A2799 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A2801 " --> pdb=" O GLN A2762 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A2764 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A2803 " --> pdb=" O HIS A2764 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A2766 " --> pdb=" O VAL A2803 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLY A2841 " --> pdb=" O TYR A2798 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER A2800 " --> pdb=" O GLY A2841 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL A2843 " --> pdb=" O SER A2800 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A2802 " --> pdb=" O VAL A2843 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A2845 " --> pdb=" O VAL A2802 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A2804 " --> pdb=" O ILE A2845 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A2726 " --> pdb=" O GLY A2844 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N SER A2846 " --> pdb=" O LEU A2726 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A2728 " --> pdb=" O SER A2846 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A2727 " --> pdb=" O VAL A2861 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 3026 through 3028 removed outlier: 3.954A pdb=" N VAL A3060 " --> pdb=" O GLU A3026 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3080 through 3082 removed outlier: 4.507A pdb=" N LYS A3086 " --> pdb=" O VAL A3101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3304 through 3307 removed outlier: 6.637A pdb=" N LYS A3332 " --> pdb=" O PHE A3372 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR A3374 " --> pdb=" O LYS A3332 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A3334 " --> pdb=" O TYR A3374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A3376 " --> pdb=" O LEU A3334 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE A3336 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS A3378 " --> pdb=" O ILE A3336 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ALA A3338 " --> pdb=" O LYS A3378 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A3373 " --> pdb=" O VAL A3273 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N ARG A3397 " --> pdb=" O ALA A3272 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE A3274 " --> pdb=" O ARG A3397 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL A3399 " --> pdb=" O PHE A3274 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A3276 " --> pdb=" O VAL A3399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3958 through 3959 Processing sheet with id=AB6, first strand: chain 'A' and resid 4880 through 4883 Processing sheet with id=AB7, first strand: chain 'B' and resid 22 through 26 removed outlier: 4.492A pdb=" N ILE B 25 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN B 36 " --> pdb=" O ILE B 25 " (cutoff:3.500A) 1864 hydrogen bonds defined for protein. 5469 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: 12.44 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9615 1.33 - 1.46: 9502 1.46 - 1.59: 18110 1.59 - 1.71: 3 1.71 - 1.84: 316 Bond restraints: 37546 Sorted by residual: bond pdb=" C LYS A4310 " pdb=" N PRO A4311 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" CB MET A1811 " pdb=" CG MET A1811 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.87e+00 bond pdb=" CG ARG A2316 " pdb=" CD ARG A2316 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.90e+00 bond pdb=" C LYS A3826 " pdb=" N PRO A3827 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.79e+00 bond pdb=" CB ASN A1014 " pdb=" CG ASN A1014 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.85e+00 ... (remaining 37541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 49950 4.34 - 8.68: 716 8.68 - 13.02: 96 13.02 - 17.37: 27 17.37 - 21.71: 8 Bond angle restraints: 50797 Sorted by residual: angle pdb=" CA MET A 721 " pdb=" CB MET A 721 " pdb=" CG MET A 721 " ideal model delta sigma weight residual 114.10 131.68 -17.58 2.00e+00 2.50e-01 7.72e+01 angle pdb=" N GLU A1135 " pdb=" CA GLU A1135 " pdb=" CB GLU A1135 " ideal model delta sigma weight residual 110.28 122.67 -12.39 1.55e+00 4.16e-01 6.39e+01 angle pdb=" CA MET A2012 " pdb=" CB MET A2012 " pdb=" CG MET A2012 " ideal model delta sigma weight residual 114.10 129.74 -15.64 2.00e+00 2.50e-01 6.11e+01 angle pdb=" CA GLN A5121 " pdb=" CB GLN A5121 " pdb=" CG GLN A5121 " ideal model delta sigma weight residual 114.10 129.19 -15.09 2.00e+00 2.50e-01 5.69e+01 angle pdb=" C ARG A3000 " pdb=" N TYR A3001 " pdb=" CA TYR A3001 " ideal model delta sigma weight residual 121.54 134.92 -13.38 1.91e+00 2.74e-01 4.91e+01 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21389 17.96 - 35.93: 1245 35.93 - 53.89: 169 53.89 - 71.86: 45 71.86 - 89.82: 19 Dihedral angle restraints: 22867 sinusoidal: 9402 harmonic: 13465 Sorted by residual: dihedral pdb=" CA VAL A3122 " pdb=" C VAL A3122 " pdb=" N PRO A3123 " pdb=" CA PRO A3123 " ideal model delta harmonic sigma weight residual 180.00 120.90 59.10 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA GLU A1170 " pdb=" C GLU A1170 " pdb=" N ALA A1171 " pdb=" CA ALA A1171 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+01 dihedral pdb=" CA GLU A4165 " pdb=" C GLU A4165 " pdb=" N PRO A4166 " pdb=" CA PRO A4166 " ideal model delta harmonic sigma weight residual -180.00 -137.10 -42.90 0 5.00e+00 4.00e-02 7.36e+01 ... (remaining 22864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5039 0.104 - 0.208: 591 0.208 - 0.312: 62 0.312 - 0.416: 21 0.416 - 0.520: 6 Chirality restraints: 5719 Sorted by residual: chirality pdb=" CA GLN A5121 " pdb=" N GLN A5121 " pdb=" C GLN A5121 " pdb=" CB GLN A5121 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" CB ILE A2830 " pdb=" CA ILE A2830 " pdb=" CG1 ILE A2830 " pdb=" CG2 ILE A2830 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA LYS A3826 " pdb=" N LYS A3826 " pdb=" C LYS A3826 " pdb=" CB LYS A3826 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.30e+00 ... (remaining 5716 not shown) Planarity restraints: 6499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 615 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ASP A 615 " -0.082 2.00e-02 2.50e+03 pdb=" O ASP A 615 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 616 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A3122 " -0.069 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A3123 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO A3123 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A3123 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A2312 " -0.044 2.00e-02 2.50e+03 3.14e-02 1.72e+01 pdb=" CG PHE A2312 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A2312 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A2312 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A2312 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A2312 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A2312 " -0.019 2.00e-02 2.50e+03 ... (remaining 6496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 962 2.70 - 3.25: 35346 3.25 - 3.80: 58149 3.80 - 4.35: 75068 4.35 - 4.90: 121849 Nonbonded interactions: 291374 Sorted by model distance: nonbonded pdb=" O2B ATP A5201 " pdb="MG MG A5202 " model vdw 2.148 2.170 nonbonded pdb=" OE2 GLU A2060 " pdb="MG MG A5202 " model vdw 2.174 2.170 nonbonded pdb=" OG1 THR A1820 " pdb=" OD1 ASP A1822 " model vdw 2.238 3.040 nonbonded pdb=" O SER A3790 " pdb=" OG SER A3793 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR A2513 " pdb=" OD2 ASP A2812 " model vdw 2.280 3.040 ... (remaining 291369 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 42.140 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.020 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.006 0.097 37556 Z= 0.268 Angle : 1.317 21.707 50810 Z= 0.669 Chirality : 0.072 0.520 5719 Planarity : 0.008 0.106 6499 Dihedral : 12.056 89.824 14093 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.91 % Favored : 90.94 % Rotamer: Outliers : 0.02 % Allowed : 1.34 % Favored : 98.64 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.09 % 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: -3.74 (0.10), residues: 4545 helix: -2.12 (0.08), residues: 2558 sheet: -1.22 (0.29), residues: 263 loop : -3.11 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 710 TYR 0.061 0.003 TYR A1277 PHE 0.067 0.003 PHE A2312 TRP 0.060 0.003 TRP A3832 HIS 0.020 0.002 HIS A4587 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.27 (37546) covalent geometry : angle 1.31319 / 0.67 (50797) SS BOND : bond 0.00383 / 0.19 ( 2) SS BOND : angle 5.72875 / 2.89 ( 4) hydrogen bonds : bond 0.13297 / 8.40 ( 1864) hydrogen bonds : angle 6.63231 / 4.57 ( 5469) metal coordination : bond 0.00995 / 0.44 ( 8) metal coordination : angle 6.96036 / 3.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.8734 (tmm) cc_final: 0.8232 (mmt) REVERT: A 622 ILE cc_start: 0.7500 (pt) cc_final: 0.7106 (pt) REVERT: A 763 ASP cc_start: 0.8431 (m-30) cc_final: 0.8141 (m-30) REVERT: A 994 ASP cc_start: 0.8326 (t70) cc_final: 0.8094 (t70) REVERT: A 1031 TRP cc_start: 0.7955 (t-100) cc_final: 0.7660 (t-100) REVERT: A 1084 GLU cc_start: 0.9178 (pt0) cc_final: 0.8951 (pp20) REVERT: A 1095 ASP cc_start: 0.8116 (m-30) cc_final: 0.7812 (m-30) REVERT: A 1117 LEU cc_start: 0.9520 (mm) cc_final: 0.9040 (pp) REVERT: A 1121 ARG cc_start: 0.9611 (ttp-110) cc_final: 0.9354 (ttp-110) REVERT: A 1313 HIS cc_start: 0.9047 (m90) cc_final: 0.8818 (m170) REVERT: A 1314 GLN cc_start: 0.9202 (tp40) cc_final: 0.8931 (tp40) REVERT: A 1462 LEU cc_start: 0.7984 (tp) cc_final: 0.7776 (tt) REVERT: A 1740 LEU cc_start: 0.9561 (mp) cc_final: 0.9356 (mt) REVERT: A 2115 MET cc_start: 0.7423 (ppp) cc_final: 0.7214 (ppp) REVERT: A 2273 HIS cc_start: 0.7541 (m90) cc_final: 0.7094 (m90) REVERT: A 2274 MET cc_start: 0.7949 (mmp) cc_final: 0.7634 (mmp) REVERT: A 2361 MET cc_start: 0.8826 (mpp) cc_final: 0.8574 (mpp) REVERT: A 2816 MET cc_start: 0.8527 (pmm) cc_final: 0.8241 (pmm) REVERT: A 3539 GLU cc_start: 0.8863 (pp20) cc_final: 0.8596 (pp20) REVERT: A 4319 LEU cc_start: 0.9509 (mt) cc_final: 0.9309 (mt) REVERT: A 4322 TYR cc_start: 0.8797 (t80) cc_final: 0.8326 (t80) REVERT: A 4392 MET cc_start: 0.9660 (ptp) cc_final: 0.9419 (mpp) REVERT: A 4954 ILE cc_start: 0.8425 (mm) cc_final: 0.8210 (mm) REVERT: A 5024 PHE cc_start: 0.9073 (t80) cc_final: 0.8723 (t80) outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.2323 time to fit residues: 120.7526 Evaluate side-chains 217 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4701 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 ASN ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 HIS ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1518 GLN A1791 GLN A2126 GLN A2136 HIS A2270 ASN ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3065 GLN A3119 GLN A3337 GLN A4001 HIS A4134 GLN A4263 GLN ** A4276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4873 ASN ** A4892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5017 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.063589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.048679 restraints weight = 272890.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.049967 restraints weight = 146476.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050820 restraints weight = 96732.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.051347 restraints weight = 73194.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.051738 restraints weight = 60881.916| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37556 Z= 0.210 Angle : 0.761 13.043 50810 Z= 0.388 Chirality : 0.044 0.217 5719 Planarity : 0.005 0.084 6499 Dihedral : 5.817 58.022 4947 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.03 % Favored : 91.93 % Rotamer: Outliers : 0.66 % Allowed : 6.43 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % 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: -1.73 (0.12), residues: 4545 helix: -0.19 (0.10), residues: 2610 sheet: -0.87 (0.29), residues: 296 loop : -2.77 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3919 TYR 0.033 0.002 TYR A1133 PHE 0.038 0.002 PHE A2312 TRP 0.023 0.002 TRP A3832 HIS 0.009 0.001 HIS A3588 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (37546) covalent geometry : angle 0.75749 / 0.39 (50797) SS BOND : bond 0.00333 / 0.16 ( 2) SS BOND : angle 2.80995 / 1.43 ( 4) hydrogen bonds : bond 0.04008 / 2.62 ( 1864) hydrogen bonds : angle 4.71329 / 3.26 ( 5469) metal coordination : bond 0.00689 / 0.36 ( 8) metal coordination : angle 4.97994 / 2.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 1.439 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: A 601 MET cc_start: 0.7264 (ttt) cc_final: 0.6911 (ppp) REVERT: A 763 ASP cc_start: 0.8633 (m-30) cc_final: 0.8362 (m-30) REVERT: A 783 MET cc_start: 0.8751 (mpp) cc_final: 0.8394 (mpp) REVERT: A 795 MET cc_start: 0.7274 (mmp) cc_final: 0.6979 (mmp) REVERT: A 909 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7935 (tmm) REVERT: A 994 ASP cc_start: 0.8630 (t70) cc_final: 0.8386 (t70) REVERT: A 1031 TRP cc_start: 0.8210 (t-100) cc_final: 0.7946 (t-100) REVERT: A 1095 ASP cc_start: 0.8412 (m-30) cc_final: 0.8065 (m-30) REVERT: A 1117 LEU cc_start: 0.9577 (mm) cc_final: 0.9070 (pp) REVERT: A 1121 ARG cc_start: 0.9631 (ttp-110) cc_final: 0.9366 (ttp-110) REVERT: A 1132 ARG cc_start: 0.9283 (ptt180) cc_final: 0.8986 (ptt90) REVERT: A 1313 HIS cc_start: 0.9134 (m-70) cc_final: 0.8676 (m90) REVERT: A 1314 GLN cc_start: 0.9153 (tp40) cc_final: 0.8938 (tp40) REVERT: A 2307 MET cc_start: 0.9054 (tpp) cc_final: 0.8799 (tpp) REVERT: A 2380 MET cc_start: 0.7947 (tpt) cc_final: 0.7607 (tpt) REVERT: A 3265 MET cc_start: 0.8153 (tpt) cc_final: 0.7863 (tpt) REVERT: A 3615 TYR cc_start: 0.8439 (t80) cc_final: 0.8230 (t80) REVERT: A 3731 MET cc_start: 0.8499 (tmm) cc_final: 0.7918 (tmm) REVERT: A 4322 TYR cc_start: 0.8699 (t80) cc_final: 0.8162 (t80) REVERT: A 4537 MET cc_start: 0.6022 (mtt) cc_final: 0.5741 (mtp) REVERT: A 5128 MET cc_start: 0.8061 (tmm) cc_final: 0.7702 (tmm) outliers start: 27 outliers final: 14 residues processed: 240 average time/residue: 0.2063 time to fit residues: 85.7822 Evaluate side-chains 211 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1717 TYR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 3049 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4856 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 163 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 371 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 293 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 211 optimal weight: 0.8980 chunk 450 optimal weight: 0.9980 chunk 444 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 GLN A2126 GLN ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3065 GLN ** A3095 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 GLN ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4842 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.065411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049726 restraints weight = 260754.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.050895 restraints weight = 140017.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.051695 restraints weight = 94521.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.052113 restraints weight = 74766.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.052329 restraints weight = 64892.270| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37556 Z= 0.115 Angle : 0.665 13.055 50810 Z= 0.329 Chirality : 0.042 0.232 5719 Planarity : 0.004 0.081 6499 Dihedral : 5.279 44.609 4944 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.57 % Favored : 92.41 % Rotamer: Outliers : 1.00 % Allowed : 8.36 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % 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: -1.08 (0.12), residues: 4545 helix: 0.41 (0.10), residues: 2622 sheet: -0.82 (0.29), residues: 297 loop : -2.58 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1101 TYR 0.022 0.001 TYR A3652 PHE 0.034 0.001 PHE A1286 TRP 0.017 0.001 TRP A 912 HIS 0.006 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (37546) covalent geometry : angle 0.66252 / 0.33 (50797) SS BOND : bond 0.01639 / 0.86 ( 2) SS BOND : angle 2.33712 / 1.23 ( 4) hydrogen bonds : bond 0.03517 / 2.29 ( 1864) hydrogen bonds : angle 4.36750 / 3.02 ( 5469) metal coordination : bond 0.00291 / 0.16 ( 8) metal coordination : angle 4.36078 / 2.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.846 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: A 763 ASP cc_start: 0.8092 (m-30) cc_final: 0.7813 (m-30) REVERT: A 783 MET cc_start: 0.8924 (mpp) cc_final: 0.8595 (mpp) REVERT: A 795 MET cc_start: 0.7097 (mmp) cc_final: 0.6877 (mmp) REVERT: A 888 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6330 (pt) REVERT: A 889 PHE cc_start: 0.7930 (m-80) cc_final: 0.7250 (m-80) REVERT: A 994 ASP cc_start: 0.8478 (t70) cc_final: 0.8237 (t70) REVERT: A 1031 TRP cc_start: 0.8012 (t-100) cc_final: 0.7735 (t-100) REVERT: A 1095 ASP cc_start: 0.8278 (m-30) cc_final: 0.7948 (m-30) REVERT: A 1117 LEU cc_start: 0.9608 (mm) cc_final: 0.9157 (pp) REVERT: A 1121 ARG cc_start: 0.9624 (ttp-110) cc_final: 0.9350 (ttp-110) REVERT: A 1129 GLN cc_start: 0.8904 (pp30) cc_final: 0.8664 (pp30) REVERT: A 1211 ASP cc_start: 0.8679 (m-30) cc_final: 0.8472 (p0) REVERT: A 1313 HIS cc_start: 0.9109 (m-70) cc_final: 0.8743 (m-70) REVERT: A 1314 GLN cc_start: 0.9227 (tp40) cc_final: 0.8958 (tp40) REVERT: A 1455 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8753 (mt) REVERT: A 2307 MET cc_start: 0.9076 (tpp) cc_final: 0.8863 (tpp) REVERT: A 2380 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7738 (tpt) REVERT: A 2816 MET cc_start: 0.8459 (pmm) cc_final: 0.8193 (pmm) REVERT: A 3265 MET cc_start: 0.8234 (tpt) cc_final: 0.7973 (tpp) REVERT: A 3731 MET cc_start: 0.8519 (tmm) cc_final: 0.8047 (tmm) REVERT: A 3884 LEU cc_start: 0.9387 (tt) cc_final: 0.9182 (tt) REVERT: A 4026 MET cc_start: 0.8504 (mtt) cc_final: 0.8065 (mpp) REVERT: A 4270 MET cc_start: 0.8261 (tpt) cc_final: 0.7963 (tpt) REVERT: A 4317 LEU cc_start: 0.9551 (mt) cc_final: 0.9268 (pp) REVERT: A 4322 TYR cc_start: 0.8808 (t80) cc_final: 0.8293 (t80) REVERT: A 5128 MET cc_start: 0.7878 (tmm) cc_final: 0.7598 (tmm) outliers start: 41 outliers final: 16 residues processed: 255 average time/residue: 0.2127 time to fit residues: 92.8976 Evaluate side-chains 223 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 900 TYR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1785 LYS Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4856 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 298 optimal weight: 3.9990 chunk 379 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 749 ASN A 796 HIS ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2907 GLN ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4842 GLN ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4892 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.063324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.048250 restraints weight = 273451.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.049524 restraints weight = 144963.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.050383 restraints weight = 95531.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.050955 restraints weight = 71935.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.051266 restraints weight = 59730.872| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37556 Z= 0.161 Angle : 0.670 14.121 50810 Z= 0.335 Chirality : 0.042 0.202 5719 Planarity : 0.004 0.073 6499 Dihedral : 5.137 40.351 4944 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.07 % Favored : 91.90 % Rotamer: Outliers : 1.27 % Allowed : 9.82 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % 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: -0.65 (0.13), residues: 4545 helix: 0.76 (0.10), residues: 2632 sheet: -0.75 (0.29), residues: 292 loop : -2.42 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 644 TYR 0.018 0.001 TYR A1309 PHE 0.033 0.002 PHE A2371 TRP 0.013 0.001 TRP A3832 HIS 0.006 0.001 HIS A3588 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (37546) covalent geometry : angle 0.66690 / 0.33 (50797) SS BOND : bond 0.00257 / 0.13 ( 2) SS BOND : angle 1.76790 / 0.90 ( 4) hydrogen bonds : bond 0.03483 / 2.28 ( 1864) hydrogen bonds : angle 4.26888 / 2.96 ( 5469) metal coordination : bond 0.00408 / 0.24 ( 8) metal coordination : angle 4.40853 / 2.14 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 213 time to evaluate : 1.482 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: A 525 MET cc_start: 0.9162 (ppp) cc_final: 0.8673 (mtt) REVERT: A 600 PHE cc_start: 0.3758 (m-10) cc_final: 0.2356 (m-80) REVERT: A 763 ASP cc_start: 0.8506 (m-30) cc_final: 0.8212 (m-30) REVERT: A 783 MET cc_start: 0.8904 (mpp) cc_final: 0.8527 (mpp) REVERT: A 793 MET cc_start: 0.8707 (tpp) cc_final: 0.8392 (tpp) REVERT: A 795 MET cc_start: 0.7125 (mmp) cc_final: 0.6842 (mmp) REVERT: A 888 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6420 (pt) REVERT: A 889 PHE cc_start: 0.7791 (m-80) cc_final: 0.7163 (m-80) REVERT: A 994 ASP cc_start: 0.8630 (t70) cc_final: 0.8379 (t70) REVERT: A 1031 TRP cc_start: 0.8113 (t-100) cc_final: 0.7736 (t-100) REVERT: A 1117 LEU cc_start: 0.9603 (mm) cc_final: 0.9309 (pp) REVERT: A 1129 GLN cc_start: 0.8920 (pp30) cc_final: 0.8633 (pp30) REVERT: A 1247 ASP cc_start: 0.9446 (m-30) cc_final: 0.8842 (p0) REVERT: A 1309 TYR cc_start: 0.9657 (t80) cc_final: 0.9350 (t80) REVERT: A 1313 HIS cc_start: 0.9179 (m-70) cc_final: 0.8712 (m90) REVERT: A 1314 GLN cc_start: 0.9202 (tp40) cc_final: 0.8926 (tp40) REVERT: A 1455 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8677 (mt) REVERT: A 1462 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 1556 MET cc_start: 0.8930 (tpp) cc_final: 0.8704 (tpp) REVERT: A 1764 LEU cc_start: 0.9263 (mm) cc_final: 0.9034 (mm) REVERT: A 2380 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7928 (tpt) REVERT: A 2816 MET cc_start: 0.8622 (pmm) cc_final: 0.8289 (pmm) REVERT: A 3265 MET cc_start: 0.8463 (tpt) cc_final: 0.8113 (tpp) REVERT: A 3395 LEU cc_start: 0.8585 (mm) cc_final: 0.8357 (mm) REVERT: A 3529 MET cc_start: 0.9264 (tmm) cc_final: 0.8935 (tmm) REVERT: A 3615 TYR cc_start: 0.8619 (t80) cc_final: 0.8230 (t80) REVERT: A 3645 MET cc_start: 0.8863 (ppp) cc_final: 0.8663 (ppp) REVERT: A 3731 MET cc_start: 0.8735 (tmm) cc_final: 0.8288 (tmm) REVERT: A 4026 MET cc_start: 0.8813 (mtt) cc_final: 0.8314 (mpp) REVERT: A 4322 TYR cc_start: 0.8656 (t80) cc_final: 0.8136 (t80) REVERT: A 5128 MET cc_start: 0.8020 (tmm) cc_final: 0.7600 (tmm) outliers start: 52 outliers final: 29 residues processed: 253 average time/residue: 0.2171 time to fit residues: 95.2852 Evaluate side-chains 235 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 900 TYR Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1192 ASP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 3128 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4974 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 422 optimal weight: 0.0570 chunk 358 optimal weight: 5.9990 chunk 402 optimal weight: 4.9990 chunk 299 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 386 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 446 optimal weight: 0.2980 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1928 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3785 HIS ** A4276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4842 GLN ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4879 ASN B 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.066655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051910 restraints weight = 241473.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.053111 restraints weight = 135181.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053869 restraints weight = 93044.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.054379 restraints weight = 72861.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054716 restraints weight = 61932.402| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37556 Z= 0.117 Angle : 0.650 15.988 50810 Z= 0.319 Chirality : 0.042 0.264 5719 Planarity : 0.004 0.076 6499 Dihedral : 4.982 42.413 4944 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 1.51 % Allowed : 10.38 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.41 (0.13), residues: 4545 helix: 0.97 (0.10), residues: 2629 sheet: -0.63 (0.30), residues: 287 loop : -2.33 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 644 TYR 0.019 0.001 TYR A3652 PHE 0.029 0.001 PHE A2371 TRP 0.014 0.001 TRP A 912 HIS 0.007 0.001 HIS A 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (37546) covalent geometry : angle 0.64734 / 0.32 (50797) SS BOND : bond 0.00466 / 0.23 ( 2) SS BOND : angle 2.53055 / 1.30 ( 4) hydrogen bonds : bond 0.03250 / 2.12 ( 1864) hydrogen bonds : angle 4.13932 / 2.87 ( 5469) metal coordination : bond 0.00352 / 0.19 ( 8) metal coordination : angle 3.86870 / 1.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 1.482 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: A 525 MET cc_start: 0.9185 (ppp) cc_final: 0.8692 (mtt) REVERT: A 570 MET cc_start: 0.6399 (ppp) cc_final: 0.5228 (mmp) REVERT: A 735 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 763 ASP cc_start: 0.8539 (m-30) cc_final: 0.8200 (m-30) REVERT: A 795 MET cc_start: 0.7159 (mmp) cc_final: 0.6719 (mmp) REVERT: A 888 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6352 (pt) REVERT: A 889 PHE cc_start: 0.7795 (m-80) cc_final: 0.7270 (m-80) REVERT: A 934 MET cc_start: 0.7565 (mmm) cc_final: 0.7352 (mmm) REVERT: A 994 ASP cc_start: 0.8570 (t70) cc_final: 0.8300 (t70) REVERT: A 997 LYS cc_start: 0.8401 (pttt) cc_final: 0.8168 (pttt) REVERT: A 1031 TRP cc_start: 0.8062 (t-100) cc_final: 0.7745 (t-100) REVERT: A 1117 LEU cc_start: 0.9666 (mm) cc_final: 0.9221 (pp) REVERT: A 1129 GLN cc_start: 0.8973 (pp30) cc_final: 0.8698 (pp30) REVERT: A 1195 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: A 1313 HIS cc_start: 0.9144 (m-70) cc_final: 0.8641 (m90) REVERT: A 1314 GLN cc_start: 0.9157 (tp40) cc_final: 0.8911 (tp40) REVERT: A 1455 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 1556 MET cc_start: 0.8971 (tpp) cc_final: 0.8770 (tpp) REVERT: A 1764 LEU cc_start: 0.9352 (mm) cc_final: 0.9096 (mm) REVERT: A 2380 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7908 (tpt) REVERT: A 2816 MET cc_start: 0.8600 (pmm) cc_final: 0.8240 (pmm) REVERT: A 3265 MET cc_start: 0.8548 (tpt) cc_final: 0.8169 (tpp) REVERT: A 3395 LEU cc_start: 0.8485 (mm) cc_final: 0.8220 (mm) REVERT: A 3612 MET cc_start: 0.9029 (mmm) cc_final: 0.8760 (mmp) REVERT: A 3645 MET cc_start: 0.8866 (ppp) cc_final: 0.8642 (ppp) REVERT: A 3731 MET cc_start: 0.8854 (tmm) cc_final: 0.8541 (tmm) REVERT: A 3785 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8045 (t-170) REVERT: A 3824 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 4026 MET cc_start: 0.8799 (mtt) cc_final: 0.8308 (mpp) REVERT: A 4270 MET cc_start: 0.8154 (tpt) cc_final: 0.7778 (tpt) REVERT: A 4322 TYR cc_start: 0.8684 (t80) cc_final: 0.8148 (t80) REVERT: A 4829 TYR cc_start: 0.9296 (t80) cc_final: 0.9009 (t80) REVERT: A 5128 MET cc_start: 0.7956 (tmm) cc_final: 0.7500 (tmm) outliers start: 62 outliers final: 30 residues processed: 272 average time/residue: 0.2144 time to fit residues: 101.3230 Evaluate side-chains 244 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 900 TYR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2409 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 3785 HIS Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4974 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 294 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 109 optimal weight: 0.2980 chunk 152 optimal weight: 0.0570 chunk 140 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 359 optimal weight: 7.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2273 HIS ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3588 HIS A4276 HIS ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.064014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.049036 restraints weight = 268463.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.050324 restraints weight = 144121.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.051158 restraints weight = 95544.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.051661 restraints weight = 72551.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.052054 restraints weight = 60623.931| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37556 Z= 0.108 Angle : 0.647 15.140 50810 Z= 0.315 Chirality : 0.042 0.226 5719 Planarity : 0.004 0.072 6499 Dihedral : 4.820 38.053 4944 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.72 % Favored : 92.26 % Rotamer: Outliers : 1.49 % Allowed : 11.18 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.27 (0.13), residues: 4545 helix: 1.05 (0.10), residues: 2644 sheet: -0.39 (0.30), residues: 264 loop : -2.26 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1121 TYR 0.023 0.001 TYR B 147 PHE 0.037 0.001 PHE A3879 TRP 0.014 0.001 TRP A 664 HIS 0.020 0.001 HIS A3785 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (37546) covalent geometry : angle 0.64491 / 0.31 (50797) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 2.67185 / 1.42 ( 4) hydrogen bonds : bond 0.03169 / 2.06 ( 1864) hydrogen bonds : angle 4.06511 / 2.82 ( 5469) metal coordination : bond 0.00299 / 0.16 ( 8) metal coordination : angle 3.54197 / 1.71 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 GLN cc_start: 0.1363 (OUTLIER) cc_final: 0.1009 (mm-40) REVERT: A 570 MET cc_start: 0.5994 (ppp) cc_final: 0.5082 (mmp) REVERT: A 735 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8426 (pp) REVERT: A 763 ASP cc_start: 0.8373 (m-30) cc_final: 0.8021 (m-30) REVERT: A 793 MET cc_start: 0.8629 (tpp) cc_final: 0.8210 (tpp) REVERT: A 795 MET cc_start: 0.7170 (mmp) cc_final: 0.6727 (mmp) REVERT: A 888 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6280 (pt) REVERT: A 889 PHE cc_start: 0.7754 (m-80) cc_final: 0.6941 (m-80) REVERT: A 934 MET cc_start: 0.7515 (mmm) cc_final: 0.7257 (mmm) REVERT: A 994 ASP cc_start: 0.8614 (t70) cc_final: 0.8328 (t70) REVERT: A 1031 TRP cc_start: 0.7924 (t-100) cc_final: 0.7561 (t-100) REVERT: A 1129 GLN cc_start: 0.8967 (pp30) cc_final: 0.8625 (pp30) REVERT: A 1132 ARG cc_start: 0.9282 (ptt180) cc_final: 0.8922 (ptt90) REVERT: A 1247 ASP cc_start: 0.9380 (m-30) cc_final: 0.8768 (p0) REVERT: A 1313 HIS cc_start: 0.9235 (m-70) cc_final: 0.8751 (m-70) REVERT: A 1314 GLN cc_start: 0.9218 (tp40) cc_final: 0.8935 (tp40) REVERT: A 1455 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8753 (mt) REVERT: A 1556 MET cc_start: 0.8922 (tpp) cc_final: 0.8683 (tpp) REVERT: A 1745 MET cc_start: 0.9518 (mmm) cc_final: 0.9126 (mpp) REVERT: A 1764 LEU cc_start: 0.9265 (mm) cc_final: 0.9005 (mm) REVERT: A 2380 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8139 (tpt) REVERT: A 2816 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8194 (pmm) REVERT: A 2939 ASP cc_start: 0.8646 (m-30) cc_final: 0.8394 (m-30) REVERT: A 3068 TYR cc_start: 0.7472 (t80) cc_final: 0.6559 (t80) REVERT: A 3265 MET cc_start: 0.8516 (tpt) cc_final: 0.8180 (tpp) REVERT: A 3395 LEU cc_start: 0.8456 (mm) cc_final: 0.8200 (mm) REVERT: A 3529 MET cc_start: 0.9239 (tmm) cc_final: 0.8897 (tmm) REVERT: A 3612 MET cc_start: 0.9064 (mmm) cc_final: 0.8790 (mmp) REVERT: A 3645 MET cc_start: 0.8891 (ppp) cc_final: 0.8665 (ppp) REVERT: A 3731 MET cc_start: 0.8728 (tmm) cc_final: 0.8439 (tmm) REVERT: A 3824 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7555 (mt) REVERT: A 4026 MET cc_start: 0.8686 (mtt) cc_final: 0.8212 (mpp) REVERT: A 4270 MET cc_start: 0.8186 (tpt) cc_final: 0.7954 (tpt) REVERT: A 4319 LEU cc_start: 0.9625 (mm) cc_final: 0.9250 (mt) REVERT: A 4322 TYR cc_start: 0.8626 (t80) cc_final: 0.8052 (t80) REVERT: A 4829 TYR cc_start: 0.9218 (t80) cc_final: 0.8906 (t80) REVERT: A 5128 MET cc_start: 0.7891 (tmm) cc_final: 0.7472 (tmm) outliers start: 61 outliers final: 39 residues processed: 263 average time/residue: 0.1972 time to fit residues: 90.5883 Evaluate side-chains 250 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 900 TYR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1374 SER Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1785 LYS Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2371 PHE Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 2923 MET Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4974 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 277 optimal weight: 4.9990 chunk 421 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 243 optimal weight: 0.0170 chunk 386 optimal weight: 5.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3642 GLN A4252 GLN A4382 ASN ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.063776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048864 restraints weight = 267558.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.050121 restraints weight = 143825.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050953 restraints weight = 95702.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.051495 restraints weight = 72649.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.051815 restraints weight = 60588.023| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 37556 Z= 0.112 Angle : 0.656 14.725 50810 Z= 0.317 Chirality : 0.042 0.358 5719 Planarity : 0.004 0.072 6499 Dihedral : 4.749 39.478 4944 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.48 % Favored : 92.50 % Rotamer: Outliers : 1.71 % Allowed : 11.47 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.21 (0.13), residues: 4545 helix: 1.09 (0.10), residues: 2644 sheet: -0.31 (0.30), residues: 264 loop : -2.24 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.018 0.001 TYR A3652 PHE 0.030 0.001 PHE A3879 TRP 0.015 0.001 TRP A 664 HIS 0.005 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (37546) covalent geometry : angle 0.65437 / 0.32 (50797) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 2.17639 / 1.16 ( 4) hydrogen bonds : bond 0.03130 / 2.05 ( 1864) hydrogen bonds : angle 4.04552 / 2.81 ( 5469) metal coordination : bond 0.00330 / 0.18 ( 8) metal coordination : angle 3.36718 / 1.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 209 time to evaluate : 1.354 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: A 569 GLN cc_start: 0.1388 (OUTLIER) cc_final: 0.1027 (mm-40) REVERT: A 570 MET cc_start: 0.6093 (ppp) cc_final: 0.5196 (mmp) REVERT: A 735 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (pp) REVERT: A 763 ASP cc_start: 0.8290 (m-30) cc_final: 0.7939 (m-30) REVERT: A 793 MET cc_start: 0.8663 (tpp) cc_final: 0.8293 (tpp) REVERT: A 795 MET cc_start: 0.7211 (mmp) cc_final: 0.6693 (mmp) REVERT: A 888 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6407 (pt) REVERT: A 889 PHE cc_start: 0.7807 (m-80) cc_final: 0.6972 (m-80) REVERT: A 934 MET cc_start: 0.7650 (mmm) cc_final: 0.7313 (mmm) REVERT: A 994 ASP cc_start: 0.8614 (t70) cc_final: 0.8350 (t70) REVERT: A 1031 TRP cc_start: 0.7890 (t-100) cc_final: 0.7146 (t-100) REVERT: A 1117 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9309 (pp) REVERT: A 1129 GLN cc_start: 0.8972 (pp30) cc_final: 0.8616 (pp30) REVERT: A 1132 ARG cc_start: 0.9250 (ptt180) cc_final: 0.8873 (ptt90) REVERT: A 1313 HIS cc_start: 0.9264 (m-70) cc_final: 0.8777 (m-70) REVERT: A 1314 GLN cc_start: 0.9235 (tp40) cc_final: 0.8977 (tp40) REVERT: A 1382 GLU cc_start: 0.8772 (pt0) cc_final: 0.8569 (pt0) REVERT: A 1455 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8734 (mt) REVERT: A 1556 MET cc_start: 0.9015 (tpp) cc_final: 0.8764 (tpp) REVERT: A 1764 LEU cc_start: 0.9253 (mm) cc_final: 0.8981 (mm) REVERT: A 2380 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8174 (tpt) REVERT: A 2816 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8205 (pmm) REVERT: A 2939 ASP cc_start: 0.8636 (m-30) cc_final: 0.8387 (m-30) REVERT: A 3068 TYR cc_start: 0.7471 (t80) cc_final: 0.6603 (t80) REVERT: A 3265 MET cc_start: 0.8562 (tpt) cc_final: 0.8222 (tpp) REVERT: A 3395 LEU cc_start: 0.8418 (mm) cc_final: 0.8152 (mm) REVERT: A 3645 MET cc_start: 0.8926 (ppp) cc_final: 0.8716 (ppp) REVERT: A 3731 MET cc_start: 0.8788 (tmm) cc_final: 0.8464 (tmm) REVERT: A 3824 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 4026 MET cc_start: 0.8699 (mtt) cc_final: 0.8233 (mpp) REVERT: A 4319 LEU cc_start: 0.9636 (mm) cc_final: 0.9270 (mt) REVERT: A 4322 TYR cc_start: 0.8617 (t80) cc_final: 0.8055 (t80) REVERT: A 4829 TYR cc_start: 0.9255 (t80) cc_final: 0.8930 (t80) REVERT: A 4987 MET cc_start: 0.9103 (ppp) cc_final: 0.8655 (ppp) REVERT: A 5128 MET cc_start: 0.7945 (tmm) cc_final: 0.7487 (tmm) outliers start: 70 outliers final: 40 residues processed: 263 average time/residue: 0.2082 time to fit residues: 95.1345 Evaluate side-chains 247 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1442 MET Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1785 LYS Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3531 LEU Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3678 THR Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4974 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 452 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 446 optimal weight: 0.0040 chunk 363 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2126 GLN ** A2439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2982 ASN ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3066 ASN A3119 GLN A3126 ASN ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4249 HIS A4252 GLN ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4842 GLN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.061898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047157 restraints weight = 275372.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.048387 restraints weight = 147078.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.049205 restraints weight = 97421.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.049710 restraints weight = 73784.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.050087 restraints weight = 61683.529| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37556 Z= 0.191 Angle : 0.712 14.330 50810 Z= 0.352 Chirality : 0.044 0.324 5719 Planarity : 0.004 0.070 6499 Dihedral : 4.906 38.795 4944 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.12 % Favored : 91.86 % Rotamer: Outliers : 1.49 % Allowed : 11.60 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.23 (0.13), residues: 4545 helix: 1.06 (0.10), residues: 2640 sheet: -0.51 (0.30), residues: 273 loop : -2.17 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1720 TYR 0.020 0.002 TYR A1309 PHE 0.029 0.002 PHE A 998 TRP 0.038 0.002 TRP A3832 HIS 0.005 0.001 HIS A4503 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (37546) covalent geometry : angle 0.70975 / 0.35 (50797) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 2.12801 / 1.09 ( 4) hydrogen bonds : bond 0.03420 / 2.25 ( 1864) hydrogen bonds : angle 4.22170 / 2.94 ( 5469) metal coordination : bond 0.00604 / 0.32 ( 8) metal coordination : angle 3.65573 / 1.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.509 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: A 569 GLN cc_start: 0.1463 (OUTLIER) cc_final: 0.1066 (mm-40) REVERT: A 570 MET cc_start: 0.6439 (ppp) cc_final: 0.5377 (mmp) REVERT: A 735 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 763 ASP cc_start: 0.8349 (m-30) cc_final: 0.8022 (m-30) REVERT: A 795 MET cc_start: 0.7131 (mmp) cc_final: 0.6568 (mmp) REVERT: A 889 PHE cc_start: 0.7635 (m-80) cc_final: 0.6969 (m-80) REVERT: A 994 ASP cc_start: 0.8590 (t70) cc_final: 0.8382 (t70) REVERT: A 997 LYS cc_start: 0.8476 (pttt) cc_final: 0.8251 (pttt) REVERT: A 1031 TRP cc_start: 0.7898 (t-100) cc_final: 0.7121 (t-100) REVERT: A 1117 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9313 (pp) REVERT: A 1121 ARG cc_start: 0.9537 (ptt90) cc_final: 0.9271 (ptt90) REVERT: A 1129 GLN cc_start: 0.9005 (pp30) cc_final: 0.8618 (pp30) REVERT: A 1132 ARG cc_start: 0.9264 (ptt180) cc_final: 0.8916 (ptt90) REVERT: A 1247 ASP cc_start: 0.9392 (m-30) cc_final: 0.8843 (p0) REVERT: A 1314 GLN cc_start: 0.9281 (tp40) cc_final: 0.9060 (tp40) REVERT: A 1382 GLU cc_start: 0.8830 (pt0) cc_final: 0.8606 (pt0) REVERT: A 1455 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 1556 MET cc_start: 0.9046 (tpp) cc_final: 0.8781 (tpp) REVERT: A 1764 LEU cc_start: 0.9289 (mm) cc_final: 0.9025 (mm) REVERT: A 2307 MET cc_start: 0.8360 (tpp) cc_final: 0.8062 (tpp) REVERT: A 2380 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8079 (tpt) REVERT: A 2816 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8330 (pmm) REVERT: A 2939 ASP cc_start: 0.8611 (m-30) cc_final: 0.8365 (m-30) REVERT: A 3265 MET cc_start: 0.8545 (tpt) cc_final: 0.8201 (tpp) REVERT: A 3529 MET cc_start: 0.9225 (tmm) cc_final: 0.8866 (tmm) REVERT: A 3645 MET cc_start: 0.9049 (ppp) cc_final: 0.8736 (ppp) REVERT: A 3731 MET cc_start: 0.8725 (tmm) cc_final: 0.8451 (tmm) REVERT: A 3824 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 4026 MET cc_start: 0.8786 (mtt) cc_final: 0.8364 (mpp) REVERT: A 4270 MET cc_start: 0.8107 (tpt) cc_final: 0.7886 (tpt) REVERT: A 4317 LEU cc_start: 0.9648 (mm) cc_final: 0.9259 (pp) REVERT: A 4987 MET cc_start: 0.9156 (ppp) cc_final: 0.8804 (ppp) REVERT: A 5128 MET cc_start: 0.8342 (tmm) cc_final: 0.7708 (tmm) outliers start: 61 outliers final: 42 residues processed: 256 average time/residue: 0.2131 time to fit residues: 94.1745 Evaluate side-chains 247 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 998 PHE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1442 MET Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1485 VAL Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1785 LYS Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2380 MET Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3531 LEU Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4574 LEU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain A residue 4974 THR Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 345 optimal weight: 2.9990 chunk 409 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 438 optimal weight: 7.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** A2677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3119 GLN ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4713 HIS A4842 GLN ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.062834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.048029 restraints weight = 272931.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049310 restraints weight = 144856.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.050154 restraints weight = 95406.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.050686 restraints weight = 72021.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.051073 restraints weight = 59912.796| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37556 Z= 0.119 Angle : 0.688 15.244 50810 Z= 0.331 Chirality : 0.043 0.375 5719 Planarity : 0.004 0.070 6499 Dihedral : 4.811 41.235 4944 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 1.39 % Allowed : 12.13 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: 4545 helix: 1.12 (0.10), residues: 2648 sheet: -0.49 (0.30), residues: 279 loop : -2.15 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 663 TYR 0.028 0.001 TYR A4316 PHE 0.026 0.001 PHE A2371 TRP 0.027 0.001 TRP A3832 HIS 0.006 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (37546) covalent geometry : angle 0.68685 / 0.33 (50797) SS BOND : bond 0.00035 / 0.02 ( 2) SS BOND : angle 1.74948 / 0.91 ( 4) hydrogen bonds : bond 0.03193 / 2.09 ( 1864) hydrogen bonds : angle 4.12258 / 2.86 ( 5469) metal coordination : bond 0.00421 / 0.22 ( 8) metal coordination : angle 3.16256 / 1.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 1.090 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: A 569 GLN cc_start: 0.1321 (OUTLIER) cc_final: 0.0983 (mm-40) REVERT: A 570 MET cc_start: 0.6374 (ppp) cc_final: 0.5350 (mmp) REVERT: A 735 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (pp) REVERT: A 763 ASP cc_start: 0.8270 (m-30) cc_final: 0.7932 (m-30) REVERT: A 793 MET cc_start: 0.8640 (tpp) cc_final: 0.8250 (tpp) REVERT: A 795 MET cc_start: 0.7075 (mmp) cc_final: 0.6483 (mmp) REVERT: A 889 PHE cc_start: 0.7702 (m-80) cc_final: 0.6976 (m-80) REVERT: A 934 MET cc_start: 0.6914 (mmm) cc_final: 0.6651 (mmm) REVERT: A 994 ASP cc_start: 0.8577 (t70) cc_final: 0.8166 (t70) REVERT: A 1031 TRP cc_start: 0.7783 (t-100) cc_final: 0.7015 (t-100) REVERT: A 1117 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9265 (pp) REVERT: A 1129 GLN cc_start: 0.8983 (pp30) cc_final: 0.8619 (pp30) REVERT: A 1132 ARG cc_start: 0.9236 (ptt180) cc_final: 0.8891 (ptt90) REVERT: A 1247 ASP cc_start: 0.9363 (m-30) cc_final: 0.8781 (p0) REVERT: A 1314 GLN cc_start: 0.9241 (tp-100) cc_final: 0.9028 (tp40) REVERT: A 1382 GLU cc_start: 0.8772 (pt0) cc_final: 0.8555 (pt0) REVERT: A 1455 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8714 (mt) REVERT: A 1556 MET cc_start: 0.8950 (tpp) cc_final: 0.8711 (tpp) REVERT: A 1764 LEU cc_start: 0.9260 (mm) cc_final: 0.8990 (mm) REVERT: A 2274 MET cc_start: 0.7936 (mmp) cc_final: 0.7589 (mmp) REVERT: A 2361 MET cc_start: 0.8767 (ptp) cc_final: 0.8378 (mpp) REVERT: A 2816 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8285 (pmm) REVERT: A 2855 MET cc_start: 0.8388 (ptp) cc_final: 0.7860 (ptm) REVERT: A 2939 ASP cc_start: 0.8635 (m-30) cc_final: 0.8401 (m-30) REVERT: A 3068 TYR cc_start: 0.7424 (t80) cc_final: 0.6700 (t80) REVERT: A 3265 MET cc_start: 0.8512 (tpt) cc_final: 0.8151 (tpp) REVERT: A 3395 LEU cc_start: 0.8484 (mm) cc_final: 0.8196 (mm) REVERT: A 3529 MET cc_start: 0.9205 (tmm) cc_final: 0.8827 (tmm) REVERT: A 3645 MET cc_start: 0.9032 (ppp) cc_final: 0.8825 (ppp) REVERT: A 3731 MET cc_start: 0.8709 (tmm) cc_final: 0.8448 (tmm) REVERT: A 3824 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 4026 MET cc_start: 0.8720 (mtt) cc_final: 0.8291 (mpp) REVERT: A 4322 TYR cc_start: 0.8681 (t80) cc_final: 0.8154 (t80) REVERT: A 4829 TYR cc_start: 0.9152 (t80) cc_final: 0.8853 (t80) REVERT: A 4987 MET cc_start: 0.9098 (ppp) cc_final: 0.8725 (ppp) REVERT: A 5128 MET cc_start: 0.8228 (tmm) cc_final: 0.7562 (tmm) outliers start: 57 outliers final: 41 residues processed: 250 average time/residue: 0.2178 time to fit residues: 93.8057 Evaluate side-chains 253 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1442 MET Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 1785 LYS Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3531 LEU Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3824 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4711 LEU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4856 SER Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain B residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 225 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 329 optimal weight: 0.0970 chunk 212 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 373 optimal weight: 0.8980 chunk 386 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2126 GLN A2486 ASN ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.063373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.048474 restraints weight = 270774.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.049773 restraints weight = 143725.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050616 restraints weight = 94590.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.051191 restraints weight = 71602.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.051503 restraints weight = 59282.017| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37556 Z= 0.111 Angle : 0.695 14.778 50810 Z= 0.332 Chirality : 0.043 0.414 5719 Planarity : 0.004 0.068 6499 Dihedral : 4.697 38.804 4944 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 1.10 % Allowed : 12.47 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.11 (0.13), residues: 4545 helix: 1.15 (0.10), residues: 2644 sheet: -0.28 (0.31), residues: 255 loop : -2.13 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.021 0.001 TYR A1309 PHE 0.048 0.001 PHE A2371 TRP 0.022 0.001 TRP A3832 HIS 0.005 0.001 HIS A4224 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (37546) covalent geometry : angle 0.69330 / 0.33 (50797) SS BOND : bond 0.00112 / 0.05 ( 2) SS BOND : angle 2.77451 / 1.42 ( 4) hydrogen bonds : bond 0.03123 / 2.04 ( 1864) hydrogen bonds : angle 4.09752 / 2.84 ( 5469) metal coordination : bond 0.00317 / 0.16 ( 8) metal coordination : angle 2.76086 / 1.40 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9090 Ramachandran restraints generated. 4545 Oldfield, 0 Emsley, 4545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 1.491 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: A 569 GLN cc_start: 0.1289 (OUTLIER) cc_final: 0.0952 (mm-40) REVERT: A 570 MET cc_start: 0.6269 (ppp) cc_final: 0.5269 (mmp) REVERT: A 735 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8471 (pp) REVERT: A 763 ASP cc_start: 0.8242 (m-30) cc_final: 0.7908 (m-30) REVERT: A 793 MET cc_start: 0.8672 (tpp) cc_final: 0.8253 (tpp) REVERT: A 795 MET cc_start: 0.6959 (mmp) cc_final: 0.6322 (mmp) REVERT: A 889 PHE cc_start: 0.7675 (m-80) cc_final: 0.6580 (m-80) REVERT: A 994 ASP cc_start: 0.8692 (t70) cc_final: 0.8437 (t70) REVERT: A 1031 TRP cc_start: 0.7737 (t-100) cc_final: 0.7001 (t-100) REVERT: A 1117 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9290 (pp) REVERT: A 1121 ARG cc_start: 0.9520 (ptt90) cc_final: 0.9243 (ptt90) REVERT: A 1129 GLN cc_start: 0.8993 (pp30) cc_final: 0.8665 (pp30) REVERT: A 1132 ARG cc_start: 0.9245 (ptt180) cc_final: 0.8893 (ptt90) REVERT: A 1247 ASP cc_start: 0.9372 (m-30) cc_final: 0.8797 (p0) REVERT: A 1314 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8982 (tp40) REVERT: A 1377 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8405 (tpt-90) REVERT: A 1764 LEU cc_start: 0.9208 (mm) cc_final: 0.8932 (mm) REVERT: A 2274 MET cc_start: 0.7905 (mmp) cc_final: 0.7560 (mmp) REVERT: A 2371 PHE cc_start: 0.9064 (p90) cc_final: 0.8764 (p90) REVERT: A 2816 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8264 (pmm) REVERT: A 2939 ASP cc_start: 0.8657 (m-30) cc_final: 0.8419 (m-30) REVERT: A 3068 TYR cc_start: 0.7374 (t80) cc_final: 0.6667 (t80) REVERT: A 3265 MET cc_start: 0.8521 (tpt) cc_final: 0.8181 (tpp) REVERT: A 3395 LEU cc_start: 0.8452 (mm) cc_final: 0.8172 (mm) REVERT: A 3529 MET cc_start: 0.9201 (tmm) cc_final: 0.8802 (tmm) REVERT: A 3645 MET cc_start: 0.9016 (ppp) cc_final: 0.8808 (ppp) REVERT: A 3731 MET cc_start: 0.8727 (tmm) cc_final: 0.8446 (tmm) REVERT: A 4026 MET cc_start: 0.8695 (mtt) cc_final: 0.8264 (mpp) REVERT: A 4319 LEU cc_start: 0.9590 (mm) cc_final: 0.9288 (mt) REVERT: A 4322 TYR cc_start: 0.8711 (t80) cc_final: 0.8023 (t80) REVERT: A 4829 TYR cc_start: 0.9114 (t80) cc_final: 0.8839 (t80) REVERT: A 4987 MET cc_start: 0.9047 (ppp) cc_final: 0.8689 (ppp) REVERT: A 5128 MET cc_start: 0.8217 (tmm) cc_final: 0.7614 (tmm) outliers start: 45 outliers final: 38 residues processed: 246 average time/residue: 0.2229 time to fit residues: 94.5789 Evaluate side-chains 246 residues out of total 4117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 832 HIS Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 933 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1280 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1442 MET Chi-restraints excluded: chain A residue 1619 LEU Chi-restraints excluded: chain A residue 2024 VAL Chi-restraints excluded: chain A residue 2061 ILE Chi-restraints excluded: chain A residue 2204 THR Chi-restraints excluded: chain A residue 2211 PHE Chi-restraints excluded: chain A residue 2357 THR Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2495 MET Chi-restraints excluded: chain A residue 2543 PHE Chi-restraints excluded: chain A residue 2642 VAL Chi-restraints excluded: chain A residue 2816 MET Chi-restraints excluded: chain A residue 3655 VAL Chi-restraints excluded: chain A residue 3801 LEU Chi-restraints excluded: chain A residue 3965 VAL Chi-restraints excluded: chain A residue 4073 VAL Chi-restraints excluded: chain A residue 4267 VAL Chi-restraints excluded: chain A residue 4504 VAL Chi-restraints excluded: chain A residue 4531 LEU Chi-restraints excluded: chain A residue 4711 LEU Chi-restraints excluded: chain A residue 4747 VAL Chi-restraints excluded: chain A residue 4858 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 216 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 166 optimal weight: 0.2980 chunk 205 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.063247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.048432 restraints weight = 271192.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049710 restraints weight = 144422.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.050569 restraints weight = 95465.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.051142 restraints weight = 71924.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.051544 restraints weight = 59372.775| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 37556 Z= 0.113 Angle : 0.696 14.407 50810 Z= 0.333 Chirality : 0.043 0.399 5719 Planarity : 0.004 0.070 6499 Dihedral : 4.644 40.132 4944 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.17 % Favored : 92.81 % Rotamer: Outliers : 1.10 % Allowed : 12.59 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.07 (0.13), residues: 4545 helix: 1.18 (0.10), residues: 2650 sheet: -0.27 (0.31), residues: 267 loop : -2.13 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 663 TYR 0.018 0.001 TYR A4316 PHE 0.050 0.001 PHE A2371 TRP 0.024 0.001 TRP A3832 HIS 0.007 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (37546) covalent geometry : angle 0.69465 / 0.33 (50797) SS BOND : bond 0.00110 / 0.05 ( 2) SS BOND : angle 2.52430 / 1.28 ( 4) hydrogen bonds : bond 0.03132 / 2.05 ( 1864) hydrogen bonds : angle 4.08018 / 2.82 ( 5469) metal coordination : bond 0.00342 / 0.17 ( 8) metal coordination : angle 2.61745 / 1.34 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8483.43 seconds wall clock time: 146 minutes 49.20 seconds (8809.20 seconds total)