Starting phenix.real_space_refine on Sun Oct 25 08:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ybl_72751/10_2026/9ybl_72751.map" } resolution = 3.44 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 82 5.16 5 C 9932 2.51 5 N 2687 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15523 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3627 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 28, 'TRANS': 474} Chain breaks: 15 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 596 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ARG:plan': 13, 'ASP:plan': 8, 'GLU:plan': 12, 'PHE:plan': 7, 'GLN:plan1': 8, 'TYR:plan': 5, 'ASN:plan1': 9} Unresolved non-hydrogen planarities: 273 Chain: "A" Number of atoms: 11868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1568, 11857 Classifications: {'peptide': 1568} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1494} Chain breaks: 14 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 814 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ASP:plan': 21, 'GLU:plan': 22, 'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 6, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 351 Conformer: "B" Number of residues, atoms: 1568, 11857 Classifications: {'peptide': 1568} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PCIS': 1, 'PTRANS': 72, 'TRANS': 1494} Chain breaks: 14 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 814 Unresolved non-hydrogen dihedrals: 527 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'ASP:plan': 21, 'GLU:plan': 22, 'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 7, 'HIS:plan': 6, 'PHE:plan': 6, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 351 bond proxies already assigned to first conformer: 12060 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.32 Number of scatterers: 15523 At special positions: 0 Unit cell: (97.24, 170.17, 131.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 2 15.00 O 2820 8.00 N 2687 7.00 C 9932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3948 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 22 sheets defined 30.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 1348 through 1356 removed outlier: 3.637A pdb=" N GLN C1353 " --> pdb=" O THR C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1398 through 1402 Processing helix chain 'C' and resid 1404 through 1409 removed outlier: 3.772A pdb=" N MET C1409 " --> pdb=" O PRO C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1434 through 1442 removed outlier: 3.514A pdb=" N ILE C1438 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C1439 " --> pdb=" O LEU C1435 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C1440 " --> pdb=" O PHE C1436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C1441 " --> pdb=" O ASN C1437 " (cutoff:3.500A) Processing helix chain 'C' and resid 1469 through 1473 removed outlier: 3.639A pdb=" N LEU C1473 " --> pdb=" O ILE C1469 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1469 through 1473' Processing helix chain 'C' and resid 1494 through 1509 removed outlier: 3.670A pdb=" N ALA C1498 " --> pdb=" O SER C1494 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C1499 " --> pdb=" O ASP C1495 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C1505 " --> pdb=" O ARG C1501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C1508 " --> pdb=" O ILE C1504 " (cutoff:3.500A) Processing helix chain 'C' and resid 1529 through 1540 removed outlier: 3.805A pdb=" N SER C1536 " --> pdb=" O LYS C1532 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C1540 " --> pdb=" O SER C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1551 through 1558 Processing helix chain 'C' and resid 1577 through 1581 removed outlier: 3.826A pdb=" N VAL C1581 " --> pdb=" O GLU C1578 " (cutoff:3.500A) Processing helix chain 'C' and resid 1602 through 1607 removed outlier: 4.019A pdb=" N ILE C1606 " --> pdb=" O TRP C1602 " (cutoff:3.500A) Processing helix chain 'C' and resid 1608 through 1613 Processing helix chain 'C' and resid 1648 through 1656 Processing helix chain 'C' and resid 1704 through 1712 removed outlier: 4.344A pdb=" N ASN C1710 " --> pdb=" O SER C1706 " (cutoff:3.500A) Processing helix chain 'C' and resid 1770 through 1791 Processing helix chain 'C' and resid 1827 through 1834 Processing helix chain 'C' and resid 1851 through 1855 Processing helix chain 'C' and resid 1913 through 1925 removed outlier: 3.903A pdb=" N GLN C1919 " --> pdb=" O ARG C1915 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C1924 " --> pdb=" O GLU C1920 " (cutoff:3.500A) Processing helix chain 'C' and resid 1940 through 1943 Processing helix chain 'A' and resid 707 through 719 removed outlier: 4.015A pdb=" N GLN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.737A pdb=" N VAL A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.841A pdb=" N GLN A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.522A pdb=" N VAL A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1004 through 1010 removed outlier: 4.301A pdb=" N VAL A1008 " --> pdb=" O CYS A1004 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS A1009 " --> pdb=" O CYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1013 No H-bonds generated for 'chain 'A' and resid 1011 through 1013' Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.600A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.537A pdb=" N LYS A1056 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1053 through 1057' Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.949A pdb=" N LEU A1193 " --> pdb=" O PRO A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1245 removed outlier: 4.151A pdb=" N LEU A1243 " --> pdb=" O LYS A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 removed outlier: 3.773A pdb=" N CYS A1266 " --> pdb=" O GLU A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1291 Processing helix chain 'A' and resid 1307 through 1312 Processing helix chain 'A' and resid 1314 through 1328 removed outlier: 4.041A pdb=" N LYS A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A1328 " --> pdb=" O GLN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'A' and resid 1398 through 1402 removed outlier: 3.589A pdb=" N TYR A1402 " --> pdb=" O GLU A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.511A pdb=" N HIS A1407 " --> pdb=" O THR A1404 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A1409 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1464 through 1471 Processing helix chain 'A' and resid 1494 through 1510 removed outlier: 3.520A pdb=" N ALA A1498 " --> pdb=" O SER A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1538 Processing helix chain 'A' and resid 1549 through 1560 removed outlier: 3.510A pdb=" N ASN A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1580 Processing helix chain 'A' and resid 1645 through 1656 removed outlier: 4.140A pdb=" N GLU A1654 " --> pdb=" O PHE A1650 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A1655 " --> pdb=" O LYS A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1673 removed outlier: 3.859A pdb=" N LEU A1673 " --> pdb=" O PRO A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1706 removed outlier: 3.516A pdb=" N SER A1706 " --> pdb=" O GLY A1703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1703 through 1706' Processing helix chain 'A' and resid 1707 through 1714 Processing helix chain 'A' and resid 1770 through 1778 removed outlier: 3.530A pdb=" N LEU A1776 " --> pdb=" O LYS A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1792 Processing helix chain 'A' and resid 1792 through 1797 removed outlier: 4.368A pdb=" N LEU A1796 " --> pdb=" O PHE A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1828 through 1833 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.539A pdb=" N ILE A1868 " --> pdb=" O PRO A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 removed outlier: 3.842A pdb=" N GLU A1874 " --> pdb=" O ASN A1871 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1923 removed outlier: 3.776A pdb=" N LEU A1916 " --> pdb=" O THR A1912 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1917 " --> pdb=" O SER A1913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1959 Processing helix chain 'A' and resid 1962 through 1966 Processing helix chain 'A' and resid 1969 through 1987 removed outlier: 3.650A pdb=" N ARG A1973 " --> pdb=" O THR A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 2035 through 2039 removed outlier: 3.797A pdb=" N ARG A2039 " --> pdb=" O PRO A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2053 through 2069 removed outlier: 3.583A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A2060 " --> pdb=" O VAL A2056 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2077 removed outlier: 3.831A pdb=" N GLU A2075 " --> pdb=" O GLY A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2084 removed outlier: 3.655A pdb=" N ASP A2084 " --> pdb=" O PRO A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2089 removed outlier: 3.627A pdb=" N ILE A2088 " --> pdb=" O ASP A2084 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2084 through 2089' Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.519A pdb=" N TYR A2099 " --> pdb=" O PRO A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2106 No H-bonds generated for 'chain 'A' and resid 2104 through 2106' Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2125 through 2133 removed outlier: 4.121A pdb=" N ILE A2131 " --> pdb=" O GLN A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2139 removed outlier: 3.946A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2135 through 2139' Processing helix chain 'A' and resid 2161 through 2164 Processing helix chain 'A' and resid 2346 through 2352 removed outlier: 4.096A pdb=" N SER A2350 " --> pdb=" O TYR A2346 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2394 Processing helix chain 'A' and resid 2499 through 2521 removed outlier: 3.593A pdb=" N ARG A2514 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A2519 " --> pdb=" O LYS A2515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A2520 " --> pdb=" O GLU A2516 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2526 removed outlier: 3.665A pdb=" N VAL A2526 " --> pdb=" O ARG A2523 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 1372 through 1376 removed outlier: 5.962A pdb=" N MET C1338 " --> pdb=" O LEU C1416 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL C1418 " --> pdb=" O MET C1338 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C1447 " --> pdb=" O ARG C1483 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR C1485 " --> pdb=" O VAL C1447 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C1449 " --> pdb=" O TYR C1485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 1690 through 1697 removed outlier: 3.826A pdb=" N VAL A1679 " --> pdb=" O TYR C1733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1811 through 1814 Processing sheet with id=AA4, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AA5, first strand: chain 'C' and resid 1894 through 1895 removed outlier: 3.974A pdb=" N ALA C1937 " --> pdb=" O VAL C1946 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.833A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.527A pdb=" N VAL A1065 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A1134 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A1251 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA9, first strand: chain 'A' and resid 1373 through 1380 removed outlier: 3.505A pdb=" N MET A1335 " --> pdb=" O VAL A1389 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N LEU A1414 " --> pdb=" O ARG A1334 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A1336 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU A1416 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A1338 " --> pdb=" O LEU A1416 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A1418 " --> pdb=" O MET A1338 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A1447 " --> pdb=" O ASP A1484 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS A1486 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A1449 " --> pdb=" O HIS A1486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AB2, first strand: chain 'A' and resid 1732 through 1734 removed outlier: 3.636A pdb=" N GLY A1737 " --> pdb=" O TRP A1734 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A1762 " --> pdb=" O GLU A1753 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1741 through 1743 removed outlier: 6.567A pdb=" N ALA A1746 " --> pdb=" O TRP A1742 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB5, first strand: chain 'A' and resid 1904 through 1907 Processing sheet with id=AB6, first strand: chain 'A' and resid 1953 through 1954 Processing sheet with id=AB7, first strand: chain 'A' and resid 2140 through 2145 removed outlier: 6.281A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A2142 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A2459 " --> pdb=" O LEU A2471 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A2473 " --> pdb=" O VAL A2457 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB9, first strand: chain 'A' and resid 2201 through 2204 removed outlier: 4.719A pdb=" N LEU A2224 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2245 through 2250 removed outlier: 5.915A pdb=" N GLY A2266 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A2248 " --> pdb=" O LEU A2264 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A2264 " --> pdb=" O LEU A2248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2315 through 2319 removed outlier: 3.765A pdb=" N MET A2315 " --> pdb=" O PHE A2326 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A2317 " --> pdb=" O PHE A2324 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A2322 " --> pdb=" O CYS A2319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2354 through 2358 removed outlier: 6.809A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 4.481A pdb=" N ARG A2446 " --> pdb=" O LEU A2436 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A2438 " --> pdb=" O LEU A2444 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A2444 " --> pdb=" O ASP A2438 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1209 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: 3.40 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5036 1.34 - 1.46: 2663 1.46 - 1.58: 7975 1.58 - 1.70: 4 1.70 - 1.82: 126 Bond restraints: 15804 Sorted by residual: bond pdb=" C5 GDP A2601 " pdb=" C4 GDP A2601 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C5 GDP A2601 " pdb=" C6 GDP A2601 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C6 GDP A2601 " pdb=" N1 GDP A2601 " ideal model delta sigma weight residual 1.337 1.389 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C8 GDP A2601 " pdb=" N7 GDP A2601 " ideal model delta sigma weight residual 1.350 1.305 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" O1B GDP A2601 " pdb=" PB GDP A2601 " ideal model delta sigma weight residual 1.510 1.468 0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 15799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 20914 2.61 - 5.23: 461 5.23 - 7.84: 74 7.84 - 10.46: 16 10.46 - 13.07: 5 Bond angle restraints: 21470 Sorted by residual: angle pdb=" N HIS A1621 " pdb=" CA HIS A1621 " pdb=" C HIS A1621 " ideal model delta sigma weight residual 110.13 104.56 5.57 1.15e+00 7.56e-01 2.34e+01 angle pdb=" N ILE A1606 " pdb=" CA ILE A1606 " pdb=" C ILE A1606 " ideal model delta sigma weight residual 113.71 109.13 4.58 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C PRO A1214 " pdb=" N ALA A1215 " pdb=" CA ALA A1215 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C TRP C1734 " pdb=" N ARG C1735 " pdb=" CA ARG C1735 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CD PRO A1942 " ideal model delta sigma weight residual 120.60 110.89 9.71 2.20e+00 2.07e-01 1.95e+01 ... (remaining 21465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8681 17.94 - 35.87: 743 35.87 - 53.81: 121 53.81 - 71.75: 22 71.75 - 89.68: 7 Dihedral angle restraints: 9574 sinusoidal: 3537 harmonic: 6037 Sorted by residual: dihedral pdb=" CA ARG C1941 " pdb=" C ARG C1941 " pdb=" N PRO C1942 " pdb=" CA PRO C1942 " ideal model delta harmonic sigma weight residual -180.00 -118.67 -61.33 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA GLN A2127 " pdb=" C GLN A2127 " pdb=" N VAL A2128 " pdb=" CA VAL A2128 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ILE A1606 " pdb=" C ILE A1606 " pdb=" N MET A1607 " pdb=" CA MET A1607 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1935 0.057 - 0.114: 515 0.114 - 0.171: 85 0.171 - 0.229: 7 0.229 - 0.286: 4 Chirality restraints: 2546 Sorted by residual: chirality pdb=" CB VAL C1922 " pdb=" CA VAL C1922 " pdb=" CG1 VAL C1922 " pdb=" CG2 VAL C1922 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' GDP A2601 " pdb=" C4' GDP A2601 " pdb=" O3' GDP A2601 " pdb=" C2' GDP A2601 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE A1606 " pdb=" CA ILE A1606 " pdb=" CG1 ILE A1606 " pdb=" CG2 ILE A1606 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2543 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.092 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO A1942 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1791 " 0.029 2.00e-02 2.50e+03 2.80e-02 1.95e+01 pdb=" CG TRP C1791 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP C1791 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP C1791 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1791 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1791 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1791 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1791 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1791 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C1791 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1734 " 0.025 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP C1734 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP C1734 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C1734 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1734 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1734 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1734 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1734 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1734 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C1734 " -0.002 2.00e-02 2.50e+03 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1064 2.74 - 3.28: 15572 3.28 - 3.82: 24330 3.82 - 4.36: 28719 4.36 - 4.90: 48840 Nonbonded interactions: 118525 Sorted by model distance: nonbonded pdb=" OG SER A1769 " pdb=" OE1 GLN A1854 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A1345 " pdb=" O TYR A1419 " model vdw 2.204 3.040 nonbonded pdb=" O PRO A1881 " pdb=" OH TYR A1894 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A1089 " pdb=" OG SER A1091 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR C1402 " pdb=" ND2 ASN C1437 " model vdw 2.251 3.120 ... (remaining 118520 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.440 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.005 0.120 15804 Z= 0.207 Angle : 0.936 13.069 21470 Z= 0.466 Chirality : 0.052 0.286 2546 Planarity : 0.008 0.135 2728 Dihedral : 13.981 89.684 5626 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.35 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -3.03 (0.18), residues: 2012 helix: -1.63 (0.21), residues: 517 sheet: -1.95 (0.26), residues: 360 loop : -2.25 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1558 TYR 0.024 0.002 TYR A1402 PHE 0.017 0.002 PHE A1170 TRP 0.075 0.003 TRP C1791 HIS 0.019 0.002 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (15804) covalent geometry : angle 0.93607 / 0.47 (21470) hydrogen bonds : bond 0.18640 / 12.54 ( 457) hydrogen bonds : angle 7.97486 / 5.56 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1790 GLU cc_start: 0.8020 (pt0) cc_final: 0.7801 (tp30) REVERT: C 1944 MET cc_start: 0.5931 (ppp) cc_final: 0.5490 (ppp) REVERT: A 1069 ASP cc_start: 0.8491 (t0) cc_final: 0.8287 (t0) REVERT: A 1097 PHE cc_start: 0.7972 (p90) cc_final: 0.7627 (p90) REVERT: A 1140 HIS cc_start: 0.8010 (t-90) cc_final: 0.7763 (t70) REVERT: A 1944 MET cc_start: 0.7168 (mpp) cc_final: 0.6936 (mpp) REVERT: A 1980 ASP cc_start: 0.8548 (m-30) cc_final: 0.8206 (m-30) REVERT: A 2006 TYR cc_start: 0.7608 (t80) cc_final: 0.7072 (t80) REVERT: A 2065 ASP cc_start: 0.7642 (m-30) cc_final: 0.7149 (m-30) REVERT: A 2315 MET cc_start: 0.0169 (ptt) cc_final: -0.0636 (tmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.0924 time to fit residues: 28.8314 Evaluate side-chains 165 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1919 GLN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 GLN A2450 ASN A2502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.195774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.144259 restraints weight = 39979.716| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 6.11 r_work: 0.3410 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15804 Z= 0.202 Angle : 0.733 11.450 21470 Z= 0.367 Chirality : 0.048 0.188 2546 Planarity : 0.006 0.116 2728 Dihedral : 5.810 64.287 2180 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.75 % Favored : 88.95 % Rotamer: Outliers : 0.77 % Allowed : 7.82 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.78 (0.18), residues: 2012 helix: -1.09 (0.22), residues: 545 sheet: -2.07 (0.26), residues: 368 loop : -2.18 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1558 TYR 0.017 0.002 TYR C1733 PHE 0.020 0.002 PHE A1158 TRP 0.046 0.002 TRP C1734 HIS 0.010 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (15804) covalent geometry : angle 0.73300 / 0.37 (21470) hydrogen bonds : bond 0.04198 / 2.75 ( 457) hydrogen bonds : angle 5.99541 / 4.18 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: C 1790 GLU cc_start: 0.8550 (pt0) cc_final: 0.8266 (tp30) REVERT: C 1944 MET cc_start: 0.6013 (ppp) cc_final: 0.5519 (ppp) REVERT: A 1097 PHE cc_start: 0.8394 (p90) cc_final: 0.7952 (p90) REVERT: A 1140 HIS cc_start: 0.8168 (t-90) cc_final: 0.7893 (t70) REVERT: A 1320 ARG cc_start: 0.8445 (mpp80) cc_final: 0.8186 (ttm110) REVERT: A 1944 MET cc_start: 0.7620 (mpp) cc_final: 0.7252 (mpp) REVERT: A 1976 LEU cc_start: 0.8382 (tp) cc_final: 0.8067 (tp) REVERT: A 1980 ASP cc_start: 0.8925 (m-30) cc_final: 0.8573 (m-30) REVERT: A 2006 TYR cc_start: 0.7781 (t80) cc_final: 0.7344 (t80) REVERT: A 2011 ILE cc_start: 0.8082 (pt) cc_final: 0.7803 (tt) REVERT: A 2065 ASP cc_start: 0.7775 (m-30) cc_final: 0.7293 (m-30) REVERT: A 2120 GLN cc_start: 0.8394 (mm110) cc_final: 0.7526 (tm-30) REVERT: A 2315 MET cc_start: -0.0450 (ptt) cc_final: -0.0924 (tmm) outliers start: 12 outliers final: 10 residues processed: 180 average time/residue: 0.0895 time to fit residues: 26.4865 Evaluate side-chains 175 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1831 MET Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 2511 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [146, 29, 87, 98, 51, 50, 204, 192, 94, 178, 196] chunk 146 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 196 optimal weight: 40.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 HIS A1093 ASN ** A1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1842 ASN ** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.197097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.148272 restraints weight = 35583.674| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.61 r_work: 0.3584 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15804 Z= 0.241 Angle : 0.747 10.751 21470 Z= 0.373 Chirality : 0.048 0.189 2546 Planarity : 0.006 0.104 2728 Dihedral : 5.795 62.937 2180 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.55 % Favored : 88.20 % Rotamer: Outliers : 1.09 % Allowed : 10.19 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.72 (0.18), residues: 2012 helix: -0.93 (0.22), residues: 543 sheet: -2.25 (0.25), residues: 377 loop : -2.11 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1477 TYR 0.024 0.002 TYR A1718 PHE 0.037 0.002 PHE A2059 TRP 0.045 0.002 TRP C1734 HIS 0.008 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (15804) covalent geometry : angle 0.74701 / 0.37 (21470) hydrogen bonds : bond 0.04125 / 2.68 ( 457) hydrogen bonds : angle 5.81530 / 4.07 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1432 LYS cc_start: 0.8360 (mttp) cc_final: 0.8063 (mmtp) REVERT: C 1944 MET cc_start: 0.6076 (ppp) cc_final: 0.5825 (ppp) REVERT: A 772 ARG cc_start: 0.6832 (mmm160) cc_final: 0.6378 (mmt180) REVERT: A 1097 PHE cc_start: 0.8380 (p90) cc_final: 0.7831 (p90) REVERT: A 1140 HIS cc_start: 0.8128 (t-90) cc_final: 0.7887 (t70) REVERT: A 1355 MET cc_start: 0.8344 (mmp) cc_final: 0.7971 (mmp) REVERT: A 1944 MET cc_start: 0.7872 (mpp) cc_final: 0.7631 (mpp) REVERT: A 1980 ASP cc_start: 0.9113 (m-30) cc_final: 0.8820 (m-30) REVERT: A 2006 TYR cc_start: 0.7829 (t80) cc_final: 0.7387 (t80) REVERT: A 2065 ASP cc_start: 0.7591 (m-30) cc_final: 0.7146 (m-30) REVERT: A 2120 GLN cc_start: 0.8270 (mm110) cc_final: 0.7456 (tm-30) REVERT: A 2315 MET cc_start: -0.0321 (ptt) cc_final: -0.0874 (tmm) outliers start: 17 outliers final: 13 residues processed: 175 average time/residue: 0.0954 time to fit residues: 27.1339 Evaluate side-chains 176 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 1907 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [191, 8, 150, 132, 64, 113, 126, 1, 204, 153, 19] chunk 191 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 ASN A1577 ASN ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.199951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.155900 restraints weight = 54472.638| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 7.61 r_work: 0.3486 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15804 Z= 0.159 Angle : 0.664 10.263 21470 Z= 0.331 Chirality : 0.046 0.188 2546 Planarity : 0.005 0.098 2728 Dihedral : 5.548 62.048 2180 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.75 % Favored : 89.00 % Rotamer: Outliers : 1.79 % Allowed : 11.40 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.58 (0.18), residues: 2012 helix: -0.70 (0.23), residues: 539 sheet: -2.20 (0.26), residues: 365 loop : -2.07 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1320 TYR 0.015 0.001 TYR C1733 PHE 0.013 0.001 PHE A1816 TRP 0.036 0.002 TRP C1734 HIS 0.006 0.001 HIS C1783 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (15804) covalent geometry : angle 0.66423 / 0.33 (21470) hydrogen bonds : bond 0.03474 / 2.25 ( 457) hydrogen bonds : angle 5.47813 / 3.84 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1432 LYS cc_start: 0.8458 (mttp) cc_final: 0.8195 (mmtm) REVERT: C 1668 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8146 (tp) REVERT: C 1944 MET cc_start: 0.6278 (ppp) cc_final: 0.5993 (ppp) REVERT: A 772 ARG cc_start: 0.6768 (mmm160) cc_final: 0.6402 (mmt180) REVERT: A 1097 PHE cc_start: 0.8423 (p90) cc_final: 0.7835 (p90) REVERT: A 1140 HIS cc_start: 0.8313 (t-90) cc_final: 0.8018 (t70) REVERT: A 1355 MET cc_start: 0.8309 (mmp) cc_final: 0.8005 (mmp) REVERT: A 1429 ASP cc_start: 0.8488 (m-30) cc_final: 0.8226 (m-30) REVERT: A 1577 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8754 (t0) REVERT: A 1944 MET cc_start: 0.8001 (mpp) cc_final: 0.7783 (mpp) REVERT: A 1980 ASP cc_start: 0.9089 (m-30) cc_final: 0.8786 (m-30) REVERT: A 2006 TYR cc_start: 0.7775 (t80) cc_final: 0.7434 (t80) REVERT: A 2053 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7635 (pm20) REVERT: A 2059 PHE cc_start: 0.9093 (t80) cc_final: 0.8819 (t80) REVERT: A 2063 LEU cc_start: 0.8491 (mm) cc_final: 0.8196 (mm) REVERT: A 2065 ASP cc_start: 0.7702 (m-30) cc_final: 0.7208 (m-30) REVERT: A 2120 GLN cc_start: 0.8308 (mm110) cc_final: 0.7538 (tm-30) REVERT: A 2315 MET cc_start: -0.0455 (ptt) cc_final: -0.0834 (tmm) outliers start: 28 outliers final: 19 residues processed: 191 average time/residue: 0.0946 time to fit residues: 29.6774 Evaluate side-chains 194 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1577 ASN Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1928 HIS Chi-restraints excluded: chain A residue 2017 ASP Chi-restraints excluded: chain A residue 2106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [143, 203, 126, 45, 152, 155, 91, 128, 109, 61, 148] chunk 143 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1730 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1842 ASN A1845 GLN ** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.199284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.151225 restraints weight = 48850.943| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 6.92 r_work: 0.3505 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15804 Z= 0.166 Angle : 0.662 10.006 21470 Z= 0.330 Chirality : 0.046 0.187 2546 Planarity : 0.005 0.095 2728 Dihedral : 5.459 61.502 2180 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.60 % Favored : 89.15 % Rotamer: Outliers : 2.05 % Allowed : 12.24 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.52 (0.19), residues: 2012 helix: -0.63 (0.23), residues: 544 sheet: -2.11 (0.26), residues: 375 loop : -2.08 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1943 TYR 0.011 0.001 TYR A1527 PHE 0.020 0.002 PHE A1158 TRP 0.038 0.002 TRP C1734 HIS 0.006 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (15804) covalent geometry : angle 0.66220 / 0.33 (21470) hydrogen bonds : bond 0.03419 / 2.22 ( 457) hydrogen bonds : angle 5.40475 / 3.79 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1432 LYS cc_start: 0.8408 (mttp) cc_final: 0.8111 (mmtm) REVERT: C 1668 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8116 (tp) REVERT: C 1733 TYR cc_start: 0.8357 (m-80) cc_final: 0.8086 (m-10) REVERT: C 1944 MET cc_start: 0.6254 (ppp) cc_final: 0.5954 (ppp) REVERT: A 772 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6366 (mmt180) REVERT: A 1097 PHE cc_start: 0.8399 (p90) cc_final: 0.7784 (p90) REVERT: A 1140 HIS cc_start: 0.8290 (t-90) cc_final: 0.8081 (t70) REVERT: A 1355 MET cc_start: 0.8367 (mmp) cc_final: 0.8094 (mmp) REVERT: A 1429 ASP cc_start: 0.8347 (m-30) cc_final: 0.8073 (m-30) REVERT: A 1944 MET cc_start: 0.8004 (mpp) cc_final: 0.7767 (mpp) REVERT: A 1976 LEU cc_start: 0.8454 (tp) cc_final: 0.8123 (tp) REVERT: A 1980 ASP cc_start: 0.9007 (m-30) cc_final: 0.8699 (m-30) REVERT: A 2006 TYR cc_start: 0.7804 (t80) cc_final: 0.7512 (t80) REVERT: A 2053 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7605 (pm20) REVERT: A 2065 ASP cc_start: 0.7693 (m-30) cc_final: 0.7202 (m-30) REVERT: A 2120 GLN cc_start: 0.8296 (mm110) cc_final: 0.7529 (tm-30) REVERT: A 2315 MET cc_start: -0.0687 (ptt) cc_final: -0.0992 (tmm) REVERT: A 2458 MET cc_start: 0.5593 (mpp) cc_final: 0.5336 (mpp) outliers start: 32 outliers final: 26 residues processed: 194 average time/residue: 0.0950 time to fit residues: 30.3540 Evaluate side-chains 205 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1597 PHE Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1928 HIS Chi-restraints excluded: chain A residue 2017 ASP Chi-restraints excluded: chain A residue 2106 MET Chi-restraints excluded: chain A residue 2363 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [57, 21, 204, 5, 106, 46, 14, 58, 201, 153, 22] chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 22 optimal weight: 0.0040 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1577 ASN ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.199303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.148298 restraints weight = 38229.429| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 4.79 r_work: 0.3580 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15804 Z= 0.164 Angle : 0.659 9.972 21470 Z= 0.327 Chirality : 0.045 0.176 2546 Planarity : 0.005 0.090 2728 Dihedral : 5.393 61.239 2180 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.70 % Favored : 89.05 % Rotamer: Outliers : 2.24 % Allowed : 13.13 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.46 (0.19), residues: 2012 helix: -0.58 (0.23), residues: 550 sheet: -2.04 (0.27), residues: 372 loop : -2.06 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1477 TYR 0.012 0.001 TYR A1402 PHE 0.029 0.001 PHE A2059 TRP 0.038 0.002 TRP C1734 HIS 0.006 0.001 HIS C1783 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (15804) covalent geometry : angle 0.65869 / 0.33 (21470) hydrogen bonds : bond 0.03321 / 2.15 ( 457) hydrogen bonds : angle 5.31691 / 3.74 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1432 LYS cc_start: 0.8284 (mttp) cc_final: 0.8057 (mmtm) REVERT: C 1503 THR cc_start: 0.8101 (p) cc_final: 0.7824 (t) REVERT: C 1668 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7975 (tp) REVERT: C 1733 TYR cc_start: 0.8248 (m-80) cc_final: 0.7825 (m-10) REVERT: C 1944 MET cc_start: 0.6246 (ppp) cc_final: 0.5919 (ppp) REVERT: A 772 ARG cc_start: 0.6832 (mmm160) cc_final: 0.6389 (mmt180) REVERT: A 1097 PHE cc_start: 0.8352 (p90) cc_final: 0.7700 (p90) REVERT: A 1140 HIS cc_start: 0.8197 (t-90) cc_final: 0.7976 (t70) REVERT: A 1355 MET cc_start: 0.8362 (mmp) cc_final: 0.8071 (mmp) REVERT: A 1429 ASP cc_start: 0.8017 (m-30) cc_final: 0.7744 (m-30) REVERT: A 1577 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8729 (t0) REVERT: A 1944 MET cc_start: 0.7993 (mpp) cc_final: 0.7755 (mpp) REVERT: A 1976 LEU cc_start: 0.8492 (tp) cc_final: 0.8155 (tp) REVERT: A 1980 ASP cc_start: 0.8900 (m-30) cc_final: 0.8544 (m-30) REVERT: A 2006 TYR cc_start: 0.7885 (t80) cc_final: 0.7607 (t80) REVERT: A 2011 ILE cc_start: 0.8133 (pt) cc_final: 0.7827 (tt) REVERT: A 2065 ASP cc_start: 0.7660 (m-30) cc_final: 0.7170 (m-30) REVERT: A 2315 MET cc_start: -0.0500 (ptt) cc_final: -0.0770 (tmm) REVERT: A 2470 MET cc_start: 0.2557 (ppp) cc_final: 0.2300 (ptm) outliers start: 35 outliers final: 28 residues processed: 199 average time/residue: 0.0964 time to fit residues: 31.6046 Evaluate side-chains 206 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1452 THR Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1577 ASN Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1816 PHE Chi-restraints excluded: chain A residue 1928 HIS Chi-restraints excluded: chain A residue 2017 ASP Chi-restraints excluded: chain A residue 2106 MET Chi-restraints excluded: chain A residue 2363 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [133, 20, 101, 67, 98, 26, 169, 130, 202, 135, 95] chunk 133 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1741 ASN ** A1577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1842 ASN A1977 HIS ** A1998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 GLN A2127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.201456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.153978 restraints weight = 43033.580| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 5.82 r_work: 0.3579 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15804 Z= 0.111 Angle : 0.629 9.651 21470 Z= 0.310 Chirality : 0.044 0.173 2546 Planarity : 0.005 0.087 2728 Dihedral : 5.187 60.924 2180 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.81 % Favored : 89.95 % Rotamer: Outliers : 1.92 % Allowed : 13.97 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.35 (0.19), residues: 2012 helix: -0.46 (0.23), residues: 552 sheet: -1.94 (0.27), residues: 368 loop : -2.02 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1477 TYR 0.011 0.001 TYR A1053 PHE 0.022 0.001 PHE A1158 TRP 0.030 0.002 TRP C1734 HIS 0.004 0.001 HIS C1783 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15804) covalent geometry : angle 0.62908 / 0.31 (21470) hydrogen bonds : bond 0.03024 / 1.95 ( 457) hydrogen bonds : angle 5.14185 / 3.61 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1503 THR cc_start: 0.8083 (p) cc_final: 0.7819 (t) REVERT: C 1668 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7967 (tp) REVERT: C 1733 TYR cc_start: 0.8299 (m-80) cc_final: 0.7882 (m-10) REVERT: C 1944 MET cc_start: 0.6239 (ppp) cc_final: 0.5921 (ppp) REVERT: A 772 ARG cc_start: 0.6823 (mmm160) cc_final: 0.6402 (mmt180) REVERT: A 1097 PHE cc_start: 0.8342 (p90) cc_final: 0.7714 (p90) REVERT: A 1140 HIS cc_start: 0.8267 (t-90) cc_final: 0.8018 (t70) REVERT: A 1355 MET cc_start: 0.8284 (mmp) cc_final: 0.7748 (mmp) REVERT: A 1429 ASP cc_start: 0.8276 (m-30) cc_final: 0.8072 (m-30) REVERT: A 1660 LEU cc_start: 0.7203 (mp) cc_final: 0.6972 (mp) REVERT: A 1944 MET cc_start: 0.7991 (mpp) cc_final: 0.7772 (mpp) REVERT: A 1976 LEU cc_start: 0.8469 (tp) cc_final: 0.8142 (tp) REVERT: A 1980 ASP cc_start: 0.8992 (m-30) cc_final: 0.8699 (m-30) REVERT: A 1984 TYR cc_start: 0.8678 (t80) cc_final: 0.8452 (t80) REVERT: A 2006 TYR cc_start: 0.7838 (t80) cc_final: 0.7579 (t80) REVERT: A 2011 ILE cc_start: 0.8090 (pt) cc_final: 0.7805 (tt) REVERT: A 2065 ASP cc_start: 0.7639 (m-30) cc_final: 0.7137 (m-30) REVERT: A 2120 GLN cc_start: 0.8203 (mm110) cc_final: 0.7670 (tm-30) REVERT: A 2315 MET cc_start: -0.0515 (ptt) cc_final: -0.0753 (tmm) outliers start: 30 outliers final: 19 residues processed: 205 average time/residue: 0.0897 time to fit residues: 30.3769 Evaluate side-chains 200 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1668 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1310 HIS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1928 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [23, 69, 74, 150, 96, 189, 140, 78, 106, 30, 193] chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 189 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 193 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1577 ASN ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.201798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.156024 restraints weight = 49138.222| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 6.89 r_work: 0.3551 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15804 Z= 0.110 Angle : 0.630 10.119 21470 Z= 0.307 Chirality : 0.044 0.158 2546 Planarity : 0.005 0.086 2728 Dihedral : 5.037 61.287 2180 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.61 % Favored : 90.09 % Rotamer: Outliers : 1.67 % Allowed : 14.29 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.22 (0.19), residues: 2012 helix: -0.34 (0.23), residues: 552 sheet: -1.93 (0.27), residues: 360 loop : -1.93 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1477 TYR 0.011 0.001 TYR A1053 PHE 0.028 0.001 PHE A2059 TRP 0.029 0.002 TRP C1734 HIS 0.004 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15804) covalent geometry : angle 0.63043 / 0.31 (21470) hydrogen bonds : bond 0.02928 / 1.89 ( 457) hydrogen bonds : angle 5.04892 / 3.55 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1503 THR cc_start: 0.8086 (p) cc_final: 0.7817 (t) REVERT: C 1733 TYR cc_start: 0.8414 (m-80) cc_final: 0.7937 (m-10) REVERT: C 1944 MET cc_start: 0.6239 (ppp) cc_final: 0.5915 (ppp) REVERT: A 772 ARG cc_start: 0.6786 (mmm160) cc_final: 0.6336 (mmt180) REVERT: A 1097 PHE cc_start: 0.8348 (p90) cc_final: 0.7700 (p90) REVERT: A 1140 HIS cc_start: 0.8311 (t-90) cc_final: 0.8058 (t70) REVERT: A 1355 MET cc_start: 0.8292 (mmp) cc_final: 0.7802 (mmp) REVERT: A 1577 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8836 (t0) REVERT: A 1660 LEU cc_start: 0.7204 (mp) cc_final: 0.6978 (mp) REVERT: A 1976 LEU cc_start: 0.8451 (tp) cc_final: 0.8133 (tp) REVERT: A 1980 ASP cc_start: 0.9061 (m-30) cc_final: 0.8778 (m-30) REVERT: A 1984 TYR cc_start: 0.8721 (t80) cc_final: 0.8505 (t80) REVERT: A 1986 HIS cc_start: 0.8189 (m-70) cc_final: 0.7834 (m-70) REVERT: A 2006 TYR cc_start: 0.7837 (t80) cc_final: 0.7568 (t80) REVERT: A 2011 ILE cc_start: 0.8065 (pt) cc_final: 0.7783 (tt) REVERT: A 2065 ASP cc_start: 0.7685 (m-30) cc_final: 0.7166 (m-30) REVERT: A 2120 GLN cc_start: 0.8176 (mm110) cc_final: 0.7581 (tm-30) REVERT: A 2459 MET cc_start: 0.4633 (pmm) cc_final: 0.4308 (pmm) REVERT: A 2521 MET cc_start: 0.8970 (ppp) cc_final: 0.7638 (ppp) outliers start: 26 outliers final: 20 residues processed: 199 average time/residue: 0.0916 time to fit residues: 30.0222 Evaluate side-chains 196 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1577 ASN Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1928 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [96, 24, 148, 175, 108, 140, 75, 122, 93, 101, 183] chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 175 optimal weight: 30.0000 chunk 108 optimal weight: 0.0040 chunk 140 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 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 = 0.4698 r_free = 0.4698 target = 0.201414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.155293 restraints weight = 36252.501| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 5.18 r_work: 0.3626 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 15804 Z= 0.152 Angle : 0.824 59.199 21470 Z= 0.446 Chirality : 0.046 0.452 2546 Planarity : 0.005 0.083 2728 Dihedral : 5.043 61.352 2180 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.76 % Favored : 89.95 % Rotamer: Outliers : 1.67 % Allowed : 14.35 % Favored : 83.98 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.25 (0.19), residues: 2012 helix: -0.40 (0.23), residues: 556 sheet: -1.92 (0.27), residues: 360 loop : -1.93 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1477 TYR 0.010 0.001 TYR A1053 PHE 0.012 0.001 PHE A2059 TRP 0.029 0.002 TRP C1734 HIS 0.004 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (15804) covalent geometry : angle 0.82370 / 0.45 (21470) hydrogen bonds : bond 0.02957 / 1.92 ( 457) hydrogen bonds : angle 5.09842 / 3.57 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1503 THR cc_start: 0.8008 (p) cc_final: 0.7708 (t) REVERT: C 1607 MET cc_start: 0.8039 (tpt) cc_final: 0.7828 (tpt) REVERT: C 1733 TYR cc_start: 0.8349 (m-80) cc_final: 0.7858 (m-10) REVERT: C 1944 MET cc_start: 0.6193 (ppp) cc_final: 0.5875 (ppp) REVERT: A 772 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6432 (mmt180) REVERT: A 1097 PHE cc_start: 0.8268 (p90) cc_final: 0.7615 (p90) REVERT: A 1140 HIS cc_start: 0.8214 (t-90) cc_final: 0.7970 (t70) REVERT: A 1355 MET cc_start: 0.8306 (mmp) cc_final: 0.7799 (mmp) REVERT: A 1660 LEU cc_start: 0.7108 (mp) cc_final: 0.6904 (mp) REVERT: A 1976 LEU cc_start: 0.8570 (tp) cc_final: 0.8224 (tp) REVERT: A 1980 ASP cc_start: 0.9043 (m-30) cc_final: 0.8770 (m-30) REVERT: A 1984 TYR cc_start: 0.8525 (t80) cc_final: 0.8265 (t80) REVERT: A 1986 HIS cc_start: 0.8085 (m-70) cc_final: 0.7727 (m-70) REVERT: A 2006 TYR cc_start: 0.7924 (t80) cc_final: 0.7610 (t80) REVERT: A 2011 ILE cc_start: 0.8105 (pt) cc_final: 0.7831 (tt) REVERT: A 2065 ASP cc_start: 0.7632 (m-30) cc_final: 0.7137 (m-30) REVERT: A 2120 GLN cc_start: 0.8085 (mm110) cc_final: 0.7551 (tm-30) REVERT: A 2521 MET cc_start: 0.8952 (ppp) cc_final: 0.7556 (ppp) outliers start: 26 outliers final: 26 residues processed: 189 average time/residue: 0.0925 time to fit residues: 28.8447 Evaluate side-chains 198 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1626 ILE Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain C residue 1921 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1310 HIS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1845 GLN Chi-restraints excluded: chain A residue 1928 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [39, 118, 134, 24, 153, 144, 74, 4, 186, 29, 22] chunk 39 optimal weight: 0.4980 chunk 118 optimal weight: 0.0970 chunk 134 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 186 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 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 = 0.4701 r_free = 0.4701 target = 0.201685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.153414 restraints weight = 45216.759| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 6.11 r_work: 0.3584 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 15804 Z= 0.152 Angle : 0.824 59.199 21470 Z= 0.446 Chirality : 0.046 0.452 2546 Planarity : 0.005 0.083 2728 Dihedral : 5.043 61.352 2180 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.76 % Favored : 89.95 % Rotamer: Outliers : 1.67 % Allowed : 14.48 % Favored : 83.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.25 (0.19), residues: 2012 helix: -0.40 (0.23), residues: 556 sheet: -1.92 (0.27), residues: 360 loop : -1.93 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1477 TYR 0.010 0.001 TYR A1053 PHE 0.012 0.001 PHE A2059 TRP 0.029 0.002 TRP C1734 HIS 0.004 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (15804) covalent geometry : angle 0.82370 / 0.45 (21470) hydrogen bonds : bond 0.02957 / 1.92 ( 457) hydrogen bonds : angle 5.09842 / 3.57 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1503 THR cc_start: 0.8053 (p) cc_final: 0.7778 (t) REVERT: C 1607 MET cc_start: 0.7992 (tpt) cc_final: 0.7789 (tpt) REVERT: C 1733 TYR cc_start: 0.8375 (m-80) cc_final: 0.7883 (m-10) REVERT: C 1944 MET cc_start: 0.6201 (ppp) cc_final: 0.5877 (ppp) REVERT: A 772 ARG cc_start: 0.6833 (mmm160) cc_final: 0.6362 (mmt180) REVERT: A 1097 PHE cc_start: 0.8319 (p90) cc_final: 0.7666 (p90) REVERT: A 1140 HIS cc_start: 0.8290 (t-90) cc_final: 0.8032 (t70) REVERT: A 1355 MET cc_start: 0.8291 (mmp) cc_final: 0.7800 (mmp) REVERT: A 1660 LEU cc_start: 0.7140 (mp) cc_final: 0.6931 (mp) REVERT: A 1976 LEU cc_start: 0.8474 (tp) cc_final: 0.8148 (tp) REVERT: A 1980 ASP cc_start: 0.9039 (m-30) cc_final: 0.8754 (m-30) REVERT: A 1984 TYR cc_start: 0.8662 (t80) cc_final: 0.8388 (t80) REVERT: A 1986 HIS cc_start: 0.8178 (m-70) cc_final: 0.7800 (m-70) REVERT: A 2006 TYR cc_start: 0.7867 (t80) cc_final: 0.7582 (t80) REVERT: A 2011 ILE cc_start: 0.8071 (pt) cc_final: 0.7796 (tt) REVERT: A 2065 ASP cc_start: 0.7679 (m-30) cc_final: 0.7170 (m-30) REVERT: A 2120 GLN cc_start: 0.8157 (mm110) cc_final: 0.7573 (tm-30) REVERT: A 2521 MET cc_start: 0.8957 (ppp) cc_final: 0.7622 (ppp) outliers start: 26 outliers final: 26 residues processed: 186 average time/residue: 0.0923 time to fit residues: 28.1991 Evaluate side-chains 198 residues out of total 1870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1343 THR Chi-restraints excluded: chain C residue 1443 SER Chi-restraints excluded: chain C residue 1530 LEU Chi-restraints excluded: chain C residue 1584 HIS Chi-restraints excluded: chain C residue 1586 GLN Chi-restraints excluded: chain C residue 1626 ILE Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain C residue 1714 GLU Chi-restraints excluded: chain C residue 1734 TRP Chi-restraints excluded: chain C residue 1762 PHE Chi-restraints excluded: chain C residue 1810 LYS Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1914 LEU Chi-restraints excluded: chain C residue 1921 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1310 HIS Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1559 GLU Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1766 THR Chi-restraints excluded: chain A residue 1845 GLN Chi-restraints excluded: chain A residue 1928 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: [123, 116, 106, 138, 71, 54, 17, 40, 115, 197, 33] chunk 123 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1998 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 = 0.4701 r_free = 0.4701 target = 0.201684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.153593 restraints weight = 49382.620| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 6.66 r_work: 0.3566 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.258 15804 Z= 0.152 Angle : 0.824 59.199 21470 Z= 0.446 Chirality : 0.046 0.452 2546 Planarity : 0.005 0.083 2728 Dihedral : 5.043 61.352 2180 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.76 % Favored : 89.95 % Rotamer: Outliers : 1.67 % Allowed : 14.48 % Favored : 83.86 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -2.25 (0.19), residues: 2012 helix: -0.40 (0.23), residues: 556 sheet: -1.92 (0.27), residues: 360 loop : -1.93 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1477 TYR 0.010 0.001 TYR A1053 PHE 0.012 0.001 PHE A2059 TRP 0.029 0.002 TRP C1734 HIS 0.004 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (15804) covalent geometry : angle 0.82370 / 0.45 (21470) hydrogen bonds : bond 0.02957 / 1.92 ( 457) hydrogen bonds : angle 5.09842 / 3.57 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.36 seconds wall clock time: 78 minutes 6.27 seconds (4686.27 seconds total)