Starting phenix.real_space_refine on Fri Jul 3 20:04:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w9l_32369/07_2026/7w9l_32369.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.116 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 22 5.49 5 S 105 5.16 5 C 9855 2.51 5 N 2239 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14915 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11445 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 1369} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 119, 970 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 978 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 931 Unusual residues: {'9Z9': 1, 'LPE': 13, 'NAG': 2, 'PCW': 5, 'Y01': 6} Classifications: {'peptide': 3, 'undetermined': 27} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'LPE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.86, per 1000 atoms: 0.19 Number of scatterers: 14915 At special positions: 0 Unit cell: (132.84, 138.24, 139.32, 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 105 16.00 P 22 15.00 O 2694 8.00 N 2239 7.00 C 9855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.02 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.05 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.02 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.07 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2008 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 570.1 milliseconds 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 65.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.716A pdb=" N TYR A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.478A pdb=" N ASP A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.858A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.594A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.946A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.816A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.540A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 267 removed outlier: 3.517A pdb=" N THR A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.603A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.675A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.370A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 388 removed outlier: 3.722A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 435 removed outlier: 3.624A pdb=" N ILE A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.062A pdb=" N VAL A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 826 Processing helix chain 'A' and resid 836 through 848 removed outlier: 3.960A pdb=" N ARG A 841 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 863 Processing helix chain 'A' and resid 866 through 888 removed outlier: 4.335A pdb=" N THR A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 900 removed outlier: 4.002A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 899 " --> pdb=" O CYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 972 removed outlier: 6.761A pdb=" N GLN A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALA A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N MET A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.539A pdb=" N ALA A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1211 Processing helix chain 'A' and resid 1214 through 1218 removed outlier: 4.114A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1249 Processing helix chain 'A' and resid 1249 through 1256 removed outlier: 3.576A pdb=" N ASN A1256 " --> pdb=" O THR A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1293 removed outlier: 3.891A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1303 Proline residue: A1297 - end of helix removed outlier: 3.904A pdb=" N SER A1302 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1343 Proline residue: A1319 - end of helix removed outlier: 4.192A pdb=" N CYS A1328 " --> pdb=" O VAL A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.537A pdb=" N CYS A1370 " --> pdb=" O ASN A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1417 Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1447 removed outlier: 3.508A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1467 removed outlier: 4.061A pdb=" N LYS A1464 " --> pdb=" O PHE A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1489 removed outlier: 3.779A pdb=" N ALA A1484 " --> pdb=" O LYS A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.676A pdb=" N ASN A1514 " --> pdb=" O ASP A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1533 removed outlier: 3.770A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 Processing helix chain 'A' and resid 1576 through 1602 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1617 through 1622 Processing helix chain 'A' and resid 1623 through 1626 Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.667A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 3.674A pdb=" N MET A1688 " --> pdb=" O PHE A1684 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1768 removed outlier: 4.115A pdb=" N PHE A1738 " --> pdb=" O SER A1734 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A1766 " --> pdb=" O ASN A1762 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A1767 " --> pdb=" O PHE A1763 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A1768 " --> pdb=" O SER A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1790 removed outlier: 3.643A pdb=" N GLU A1780 " --> pdb=" O GLU A1776 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 3.725A pdb=" N SER A1803 " --> pdb=" O PHE A1799 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1824 removed outlier: 3.773A pdb=" N ILE A1824 " --> pdb=" O LYS A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1827 No H-bonds generated for 'chain 'A' and resid 1825 through 1827' Processing helix chain 'A' and resid 1838 through 1851 removed outlier: 3.661A pdb=" N ARG A1848 " --> pdb=" O ALA A1844 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A1849 " --> pdb=" O PHE A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1869 removed outlier: 4.323A pdb=" N ASP A1857 " --> pdb=" O SER A1853 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1858 " --> pdb=" O GLY A1854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 Processing helix chain 'A' and resid 1883 through 1891 removed outlier: 3.577A pdb=" N LYS A1887 " --> pdb=" O THR A1883 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.612A pdb=" N ALA B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.542A pdb=" N VAL A 331 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA4, first strand: chain 'A' and resid 1796 through 1798 Processing sheet with id=AA5, first strand: chain 'A' and resid 1829 through 1831 removed outlier: 6.772A pdb=" N MET A1830 " --> pdb=" O ILE A1880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.020A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.680A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.303A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 65 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 48 837 hydrogen bonds defined for protein. 2367 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: 2.29 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2296 1.32 - 1.45: 4163 1.45 - 1.58: 8564 1.58 - 1.71: 46 1.71 - 1.85: 172 Bond restraints: 15241 Sorted by residual: bond pdb=" C27 P5S A2017 " pdb=" C28 P5S A2017 " ideal model delta sigma weight residual 1.523 1.324 0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" C38 P5S A2017 " pdb=" O37 P5S A2017 " ideal model delta sigma weight residual 1.331 1.463 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C11 PCW A2027 " pdb=" O3 PCW A2027 " ideal model delta sigma weight residual 1.326 1.457 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C38 P5S A2002 " pdb=" O37 P5S A2002 " ideal model delta sigma weight residual 1.331 1.459 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C11 PCW A2028 " pdb=" O3 PCW A2028 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 15236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.74: 20468 6.74 - 13.48: 116 13.48 - 20.22: 2 20.22 - 26.96: 0 26.96 - 33.70: 3 Bond angle restraints: 20589 Sorted by residual: angle pdb=" C5 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 111.64 77.94 33.70 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C6 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 109.11 77.98 31.13 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C7 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 108.24 78.02 30.22 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C ILE A1351 " pdb=" CA ILE A1351 " pdb=" CB ILE A1351 " ideal model delta sigma weight residual 111.45 102.04 9.41 1.12e+00 7.97e-01 7.06e+01 angle pdb=" N SER A1770 " pdb=" CA SER A1770 " pdb=" C SER A1770 " ideal model delta sigma weight residual 108.75 120.04 -11.29 1.71e+00 3.42e-01 4.36e+01 ... (remaining 20584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 8661 32.09 - 64.17: 372 64.17 - 96.26: 30 96.26 - 128.35: 8 128.35 - 160.43: 2 Dihedral angle restraints: 9073 sinusoidal: 4031 harmonic: 5042 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 7.11 85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CA PRO A1712 " pdb=" C PRO A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta harmonic sigma weight residual 180.00 140.00 40.00 0 5.00e+00 4.00e-02 6.40e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 141.51 -48.51 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 9070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2261 0.163 - 0.326: 48 0.326 - 0.489: 5 0.489 - 0.652: 7 0.652 - 0.815: 2 Chirality restraints: 2323 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1352 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 ... (remaining 2320 not shown) Planarity restraints: 2437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 114 " 0.125 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" CG ASN B 114 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN B 114 " 0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN B 114 " -0.550 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " 0.360 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " -0.363 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG B 302 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 93 " -0.208 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" CG ASN B 93 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B 93 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 93 " 0.509 2.00e-02 2.50e+03 pdb=" C1 NAG B 301 " -0.345 2.00e-02 2.50e+03 ... (remaining 2434 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1345 2.72 - 3.27: 16243 3.27 - 3.81: 24404 3.81 - 4.36: 29666 4.36 - 4.90: 48983 Nonbonded interactions: 120641 Sorted by model distance: nonbonded pdb=" NH1 ARG A1499 " pdb=" O PRO A1500 " model vdw 2.178 3.120 nonbonded pdb=" O PRO A 149 " pdb=" OG1 THR A 152 " model vdw 2.196 3.040 nonbonded pdb=" CB LEU A1653 " pdb=" C16 LPE A2014 " model vdw 2.214 3.840 nonbonded pdb=" O SER A 973 " pdb=" OG1 THR A 977 " model vdw 2.220 3.040 nonbonded pdb=" O SER A1288 " pdb=" OG1 THR A1291 " model vdw 2.226 3.040 ... (remaining 120636 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 12.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.012 0.199 15263 Z= 0.593 Angle : 1.466 48.793 20644 Z= 0.688 Chirality : 0.073 0.815 2323 Planarity : 0.010 0.310 2429 Dihedral : 17.127 160.433 5778 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.58 % Allowed : 6.69 % Favored : 92.72 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -3.45 (0.18), residues: 1703 helix: -1.94 (0.14), residues: 970 sheet: -2.06 (0.46), residues: 116 loop : -2.68 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.033 0.002 TYR A1413 PHE 0.029 0.002 PHE B 59 TRP 0.039 0.002 TRP A1408 HIS 0.010 0.002 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.59 (15241) covalent geometry : angle 1.36364 / 0.66 (20589) SS BOND : bond 0.01470 / 1.00 ( 11) SS BOND : angle 9.47558 / 3.15 ( 22) hydrogen bonds : bond 0.16083 / 10.73 ( 837) hydrogen bonds : angle 7.25474 / 5.12 ( 2367) link_BETA1-4 : bond 0.01506 / 0.90 ( 3) link_BETA1-4 : angle 16.85612 / 11.31 ( 9) link_NAG-ASN : bond 0.06618 / 4.61 ( 8) link_NAG-ASN : angle 8.03124 / 6.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 308 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7079 (mtt) cc_final: 0.6654 (mtm) REVERT: A 95 LYS cc_start: 0.7487 (mttp) cc_final: 0.7251 (mttp) REVERT: A 108 MET cc_start: 0.7511 (tpt) cc_final: 0.7249 (tpp) REVERT: A 176 PHE cc_start: 0.8660 (t80) cc_final: 0.8155 (t80) REVERT: A 185 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8369 (mmt90) REVERT: A 189 ASN cc_start: 0.8327 (m-40) cc_final: 0.8096 (m-40) REVERT: A 243 LYS cc_start: 0.7796 (mttp) cc_final: 0.7341 (mptt) REVERT: A 247 ASP cc_start: 0.7616 (m-30) cc_final: 0.7325 (m-30) REVERT: A 265 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7565 (tp40) REVERT: A 290 MET cc_start: 0.8254 (mmm) cc_final: 0.8001 (tpp) REVERT: A 301 LYS cc_start: 0.8265 (mttt) cc_final: 0.8053 (mtpp) REVERT: A 376 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: A 414 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 885 MET cc_start: 0.8231 (ttp) cc_final: 0.7941 (ttp) REVERT: A 1244 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8318 (mttp) REVERT: A 1474 MET cc_start: 0.9105 (mtt) cc_final: 0.8690 (mtp) REVERT: A 1545 GLU cc_start: 0.7453 (tt0) cc_final: 0.7021 (tt0) REVERT: A 1597 ASP cc_start: 0.7484 (m-30) cc_final: 0.7203 (t0) REVERT: A 1863 MET cc_start: -0.1141 (tpt) cc_final: -0.1551 (ptm) REVERT: B 29 GLU cc_start: 0.7296 (pm20) cc_final: 0.7078 (pt0) REVERT: B 131 ASN cc_start: 0.8460 (t0) cc_final: 0.8169 (t0) REVERT: B 141 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7947 (ptpp) REVERT: B 162 MET cc_start: 0.7817 (mmp) cc_final: 0.7297 (mmt) outliers start: 9 outliers final: 2 residues processed: 316 average time/residue: 0.1032 time to fit residues: 48.4332 Evaluate side-chains 235 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 278 ASN A 336 ASN A 368 GLN A 766 HIS A 780 ASN A 861 ASN A 941 GLN A1191 HIS A1276 ASN A1341 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 GLN A1709 ASN B 75 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 151 ASN C 53 ASN C 70 GLN C 82 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.241111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195991 restraints weight = 26682.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.198270 restraints weight = 32543.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.199670 restraints weight = 20670.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.201250 restraints weight = 11100.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201647 restraints weight = 10306.060| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4257 r_free = 0.4257 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4257 r_free = 0.4257 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15263 Z= 0.169 Angle : 0.749 15.122 20644 Z= 0.358 Chirality : 0.044 0.218 2323 Planarity : 0.005 0.087 2429 Dihedral : 15.047 169.184 2471 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.21 % Allowed : 11.96 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.19), residues: 1703 helix: -0.13 (0.15), residues: 988 sheet: -1.90 (0.43), residues: 120 loop : -1.90 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1886 TYR 0.019 0.002 TYR C 128 PHE 0.020 0.002 PHE C 80 TRP 0.012 0.001 TRP A 190 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15241) covalent geometry : angle 0.71033 / 0.35 (20589) SS BOND : bond 0.00398 / 0.27 ( 11) SS BOND : angle 1.15152 / 0.84 ( 22) hydrogen bonds : bond 0.04631 / 3.00 ( 837) hydrogen bonds : angle 5.07503 / 3.64 ( 2367) link_BETA1-4 : bond 0.00589 / 0.32 ( 3) link_BETA1-4 : angle 4.61162 / 2.64 ( 9) link_NAG-ASN : bond 0.00755 / 0.45 ( 8) link_NAG-ASN : angle 6.39011 / 4.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6798 (mtt) cc_final: 0.6591 (mtm) REVERT: A 81 TYR cc_start: 0.8000 (t80) cc_final: 0.7560 (t80) REVERT: A 243 LYS cc_start: 0.7740 (mttp) cc_final: 0.7357 (mptt) REVERT: A 307 GLU cc_start: 0.7323 (tp30) cc_final: 0.7096 (mp0) REVERT: A 379 MET cc_start: 0.7759 (ptm) cc_final: 0.7458 (ttt) REVERT: A 1201 MET cc_start: 0.8151 (mmp) cc_final: 0.7814 (mmp) REVERT: A 1432 TYR cc_start: 0.8805 (m-80) cc_final: 0.8574 (m-80) REVERT: A 1545 GLU cc_start: 0.7235 (tt0) cc_final: 0.7013 (tt0) REVERT: A 1826 MET cc_start: 0.3221 (mpp) cc_final: 0.2883 (mpp) REVERT: A 1830 MET cc_start: 0.2636 (mtt) cc_final: 0.0354 (ttm) REVERT: B 72 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7799 (ttt180) REVERT: B 131 ASN cc_start: 0.8456 (t0) cc_final: 0.8177 (t0) REVERT: B 162 MET cc_start: 0.7673 (mmp) cc_final: 0.7231 (mmt) REVERT: B 163 MET cc_start: 0.7573 (tmm) cc_final: 0.7225 (tmm) REVERT: C 56 TYR cc_start: 0.8184 (m-80) cc_final: 0.7951 (m-80) REVERT: C 79 MET cc_start: 0.5403 (tpp) cc_final: 0.4332 (tpp) outliers start: 34 outliers final: 27 residues processed: 280 average time/residue: 0.1091 time to fit residues: 45.2015 Evaluate side-chains 244 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1582 ASP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 40.0000 chunk 140 optimal weight: 0.0770 chunk 41 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A 941 GLN A1276 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1721 HIS B 75 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 151 ASN C 118 GLN C 126 ASN C 139 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.243510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.197589 restraints weight = 35980.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200690 restraints weight = 43205.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.203820 restraints weight = 14314.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.203609 restraints weight = 9355.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.207431 restraints weight = 7622.202| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4292 r_free = 0.4292 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4292 r_free = 0.4292 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15263 Z= 0.132 Angle : 0.636 12.150 20644 Z= 0.312 Chirality : 0.040 0.145 2323 Planarity : 0.004 0.089 2429 Dihedral : 13.788 162.398 2465 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.60 % Allowed : 14.62 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1703 helix: 0.65 (0.16), residues: 989 sheet: -1.67 (0.45), residues: 120 loop : -1.55 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.022 0.001 TYR C 128 PHE 0.015 0.001 PHE B 59 TRP 0.011 0.001 TRP A1408 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15241) covalent geometry : angle 0.60615 / 0.31 (20589) SS BOND : bond 0.00333 / 0.21 ( 11) SS BOND : angle 1.14609 / 0.83 ( 22) hydrogen bonds : bond 0.04124 / 2.67 ( 837) hydrogen bonds : angle 4.68599 / 3.35 ( 2367) link_BETA1-4 : bond 0.00853 / 0.48 ( 3) link_BETA1-4 : angle 4.88139 / 3.01 ( 9) link_NAG-ASN : bond 0.00352 / 0.21 ( 8) link_NAG-ASN : angle 4.80101 / 3.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8128 (t80) cc_final: 0.7893 (t80) REVERT: A 185 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7709 (mmt180) REVERT: A 243 LYS cc_start: 0.7768 (mttp) cc_final: 0.7386 (mptt) REVERT: A 379 MET cc_start: 0.7672 (ptm) cc_final: 0.7349 (ttt) REVERT: A 742 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5555 (mtt) REVERT: A 822 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5506 (tt0) REVERT: A 1394 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 1545 GLU cc_start: 0.7166 (tt0) cc_final: 0.6914 (tt0) REVERT: A 1668 TYR cc_start: 0.8383 (m-80) cc_final: 0.8154 (m-80) REVERT: A 1826 MET cc_start: 0.2857 (mpp) cc_final: 0.2325 (mpp) REVERT: A 1830 MET cc_start: 0.2953 (mtt) cc_final: 0.0355 (ttm) REVERT: B 72 ARG cc_start: 0.8163 (ttt90) cc_final: 0.7729 (ttt180) REVERT: B 91 VAL cc_start: 0.8970 (p) cc_final: 0.8722 (m) REVERT: B 120 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: B 131 ASN cc_start: 0.8345 (t0) cc_final: 0.8068 (t0) REVERT: B 154 MET cc_start: 0.7196 (tpp) cc_final: 0.6802 (tpp) REVERT: B 162 MET cc_start: 0.7527 (mmp) cc_final: 0.7250 (mmm) REVERT: C 79 MET cc_start: 0.5449 (tpp) cc_final: 0.4391 (tpp) outliers start: 40 outliers final: 20 residues processed: 259 average time/residue: 0.1085 time to fit residues: 42.1782 Evaluate side-chains 240 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1582 ASP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 149 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 108 optimal weight: 0.8980 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 941 GLN A1276 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.242834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.198396 restraints weight = 29803.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.201735 restraints weight = 38636.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.203709 restraints weight = 16229.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.203809 restraints weight = 11127.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.204843 restraints weight = 9284.597| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4289 r_free = 0.4289 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4289 r_free = 0.4289 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15263 Z= 0.137 Angle : 0.610 10.739 20644 Z= 0.301 Chirality : 0.040 0.197 2323 Planarity : 0.004 0.092 2429 Dihedral : 13.031 157.834 2465 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.25 % Allowed : 15.53 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1703 helix: 1.02 (0.16), residues: 974 sheet: -1.60 (0.44), residues: 126 loop : -1.34 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.016 0.001 TYR A 367 PHE 0.016 0.001 PHE B 59 TRP 0.011 0.001 TRP A1408 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15241) covalent geometry : angle 0.58782 / 0.30 (20589) SS BOND : bond 0.00292 / 0.20 ( 11) SS BOND : angle 0.94759 / 0.69 ( 22) hydrogen bonds : bond 0.03908 / 2.53 ( 837) hydrogen bonds : angle 4.57865 / 3.27 ( 2367) link_BETA1-4 : bond 0.00710 / 0.39 ( 3) link_BETA1-4 : angle 4.42363 / 2.69 ( 9) link_NAG-ASN : bond 0.00520 / 0.35 ( 8) link_NAG-ASN : angle 3.93801 / 2.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7729 (mmt180) REVERT: A 243 LYS cc_start: 0.7769 (mttp) cc_final: 0.7385 (mptt) REVERT: A 379 MET cc_start: 0.7699 (ptm) cc_final: 0.7376 (ttt) REVERT: A 742 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5649 (mtt) REVERT: A 791 MET cc_start: 0.6756 (ppp) cc_final: 0.6416 (tmm) REVERT: A 812 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: A 1278 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7219 (tp) REVERT: A 1394 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 1545 GLU cc_start: 0.7309 (tt0) cc_final: 0.7042 (tt0) REVERT: A 1826 MET cc_start: 0.3062 (mpp) cc_final: 0.2544 (mpp) REVERT: A 1830 MET cc_start: 0.3237 (mtt) cc_final: 0.0756 (ttm) REVERT: B 72 ARG cc_start: 0.8251 (ttt90) cc_final: 0.7841 (ttt180) REVERT: B 91 VAL cc_start: 0.8955 (p) cc_final: 0.8732 (m) REVERT: B 131 ASN cc_start: 0.8447 (t0) cc_final: 0.8191 (t0) REVERT: B 152 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7746 (ttp-170) REVERT: B 154 MET cc_start: 0.7270 (tpp) cc_final: 0.6883 (tpp) REVERT: B 162 MET cc_start: 0.7564 (mmp) cc_final: 0.7257 (mmm) REVERT: B 163 MET cc_start: 0.7630 (tmm) cc_final: 0.7122 (tmm) REVERT: C 79 MET cc_start: 0.5334 (tpp) cc_final: 0.4385 (tpp) outliers start: 50 outliers final: 35 residues processed: 260 average time/residue: 0.1119 time to fit residues: 43.2883 Evaluate side-chains 253 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1530 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 132 optimal weight: 40.0000 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 941 GLN A1180 ASN A1276 ASN ** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 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 = 0.4671 r_free = 0.4671 target = 0.242113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.200068 restraints weight = 32419.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.204682 restraints weight = 43740.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.202306 restraints weight = 13135.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.202583 restraints weight = 10023.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.203399 restraints weight = 7041.870| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15263 Z= 0.142 Angle : 0.605 11.835 20644 Z= 0.299 Chirality : 0.039 0.192 2323 Planarity : 0.004 0.092 2429 Dihedral : 12.474 153.828 2465 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.05 % Allowed : 17.15 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1703 helix: 1.12 (0.17), residues: 980 sheet: -1.67 (0.41), residues: 132 loop : -1.30 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 838 TYR 0.027 0.001 TYR A 81 PHE 0.014 0.001 PHE B 59 TRP 0.012 0.001 TRP A1408 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15241) covalent geometry : angle 0.58559 / 0.29 (20589) SS BOND : bond 0.00275 / 0.18 ( 11) SS BOND : angle 0.83695 / 0.61 ( 22) hydrogen bonds : bond 0.03794 / 2.45 ( 837) hydrogen bonds : angle 4.53096 / 3.23 ( 2367) link_BETA1-4 : bond 0.00575 / 0.31 ( 3) link_BETA1-4 : angle 4.24500 / 2.63 ( 9) link_NAG-ASN : bond 0.00293 / 0.18 ( 8) link_NAG-ASN : angle 3.66870 / 2.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7746 (mmt180) REVERT: A 243 LYS cc_start: 0.7742 (mttp) cc_final: 0.7375 (mptt) REVERT: A 379 MET cc_start: 0.7731 (ptm) cc_final: 0.7383 (ttt) REVERT: A 791 MET cc_start: 0.6744 (ppp) cc_final: 0.6469 (tmm) REVERT: A 941 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: A 1545 GLU cc_start: 0.7208 (tt0) cc_final: 0.6946 (tt0) REVERT: A 1826 MET cc_start: 0.2788 (mpp) cc_final: 0.2243 (mpp) REVERT: A 1830 MET cc_start: 0.3139 (mtt) cc_final: 0.0648 (ttm) REVERT: B 72 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7816 (ttt180) REVERT: B 91 VAL cc_start: 0.8902 (p) cc_final: 0.8673 (m) REVERT: B 131 ASN cc_start: 0.8437 (t0) cc_final: 0.8173 (t0) REVERT: B 154 MET cc_start: 0.7229 (tpp) cc_final: 0.6855 (tpp) REVERT: B 162 MET cc_start: 0.7518 (mmp) cc_final: 0.7227 (mmm) REVERT: C 53 ASN cc_start: 0.7642 (m-40) cc_final: 0.6691 (p0) REVERT: C 79 MET cc_start: 0.5663 (tpp) cc_final: 0.4594 (tpp) outliers start: 47 outliers final: 31 residues processed: 249 average time/residue: 0.1052 time to fit residues: 39.6620 Evaluate side-chains 245 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1530 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 30.0000 chunk 157 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 ASN A 941 GLN A1276 ASN A1494 GLN ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.242177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.196849 restraints weight = 36767.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.201267 restraints weight = 48577.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.202088 restraints weight = 14709.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.202571 restraints weight = 8890.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.203292 restraints weight = 7757.251| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4249 r_free = 0.4249 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4249 r_free = 0.4249 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15263 Z= 0.137 Angle : 0.597 9.931 20644 Z= 0.294 Chirality : 0.039 0.190 2323 Planarity : 0.004 0.093 2429 Dihedral : 12.125 150.512 2465 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.05 % Allowed : 17.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1703 helix: 1.16 (0.16), residues: 983 sheet: -1.54 (0.42), residues: 131 loop : -1.25 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.022 0.001 TYR A 81 PHE 0.014 0.001 PHE B 59 TRP 0.013 0.001 TRP A1408 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (15241) covalent geometry : angle 0.57945 / 0.29 (20589) SS BOND : bond 0.00252 / 0.17 ( 11) SS BOND : angle 0.77274 / 0.56 ( 22) hydrogen bonds : bond 0.03732 / 2.40 ( 837) hydrogen bonds : angle 4.48040 / 3.18 ( 2367) link_BETA1-4 : bond 0.00673 / 0.37 ( 3) link_BETA1-4 : angle 4.02080 / 2.41 ( 9) link_NAG-ASN : bond 0.00289 / 0.18 ( 8) link_NAG-ASN : angle 3.42112 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7402 (mttp) cc_final: 0.6890 (mmtp) REVERT: A 185 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7767 (mmt180) REVERT: A 243 LYS cc_start: 0.7777 (mttp) cc_final: 0.7318 (mptt) REVERT: A 379 MET cc_start: 0.7779 (ptm) cc_final: 0.7437 (ttt) REVERT: A 1384 ASN cc_start: 0.8793 (t0) cc_final: 0.8551 (t0) REVERT: A 1394 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7998 (mt) REVERT: A 1545 GLU cc_start: 0.7214 (tt0) cc_final: 0.6951 (tt0) REVERT: A 1732 ASN cc_start: 0.8193 (t0) cc_final: 0.7913 (t0) REVERT: A 1826 MET cc_start: 0.2715 (mpp) cc_final: 0.2155 (mpp) REVERT: A 1830 MET cc_start: 0.3421 (mtt) cc_final: 0.0930 (ttm) REVERT: B 91 VAL cc_start: 0.8891 (p) cc_final: 0.8667 (m) REVERT: B 131 ASN cc_start: 0.8434 (t0) cc_final: 0.8192 (t0) REVERT: B 152 ARG cc_start: 0.7982 (ttp-170) cc_final: 0.7744 (ttp-170) REVERT: B 154 MET cc_start: 0.7313 (tpp) cc_final: 0.7010 (tpp) REVERT: B 162 MET cc_start: 0.7531 (mmp) cc_final: 0.7235 (mmm) REVERT: C 53 ASN cc_start: 0.7594 (m-40) cc_final: 0.6656 (p0) REVERT: C 79 MET cc_start: 0.5702 (tpp) cc_final: 0.4667 (tpp) outliers start: 47 outliers final: 38 residues processed: 244 average time/residue: 0.1041 time to fit residues: 38.4509 Evaluate side-chains 249 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1530 VAL Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 137 optimal weight: 40.0000 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 0.0870 chunk 41 optimal weight: 0.0060 chunk 4 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 ASN A1276 ASN ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.242001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.196237 restraints weight = 25512.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196945 restraints weight = 31162.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.199191 restraints weight = 20968.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199782 restraints weight = 11269.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.203062 restraints weight = 10001.333| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4269 r_free = 0.4269 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4269 r_free = 0.4269 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15263 Z= 0.141 Angle : 0.588 10.460 20644 Z= 0.292 Chirality : 0.039 0.189 2323 Planarity : 0.004 0.093 2429 Dihedral : 11.902 148.154 2465 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 18.52 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1703 helix: 1.22 (0.16), residues: 977 sheet: -1.46 (0.42), residues: 132 loop : -1.22 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 838 TYR 0.022 0.001 TYR A 81 PHE 0.016 0.001 PHE A 159 TRP 0.014 0.001 TRP A1408 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15241) covalent geometry : angle 0.57204 / 0.29 (20589) SS BOND : bond 0.00264 / 0.17 ( 11) SS BOND : angle 0.75003 / 0.54 ( 22) hydrogen bonds : bond 0.03701 / 2.38 ( 837) hydrogen bonds : angle 4.46700 / 3.17 ( 2367) link_BETA1-4 : bond 0.00667 / 0.37 ( 3) link_BETA1-4 : angle 3.93985 / 2.35 ( 9) link_NAG-ASN : bond 0.00273 / 0.17 ( 8) link_NAG-ASN : angle 3.29073 / 2.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7379 (mttp) cc_final: 0.6899 (mmtp) REVERT: A 185 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7776 (mmt180) REVERT: A 216 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 243 LYS cc_start: 0.7791 (mttp) cc_final: 0.7353 (mptt) REVERT: A 379 MET cc_start: 0.7630 (ptm) cc_final: 0.7318 (ttt) REVERT: A 1394 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 1545 GLU cc_start: 0.7230 (tt0) cc_final: 0.6989 (tt0) REVERT: A 1826 MET cc_start: 0.2714 (mpp) cc_final: 0.2287 (mpp) REVERT: A 1830 MET cc_start: 0.3323 (mtt) cc_final: 0.0942 (ttm) REVERT: B 91 VAL cc_start: 0.8941 (p) cc_final: 0.8702 (m) REVERT: B 131 ASN cc_start: 0.8413 (t0) cc_final: 0.8169 (t0) REVERT: B 152 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7736 (ttp-170) REVERT: B 154 MET cc_start: 0.7298 (tpp) cc_final: 0.7025 (tpp) REVERT: B 162 MET cc_start: 0.7544 (mmp) cc_final: 0.7232 (mmm) REVERT: B 163 MET cc_start: 0.7578 (tmm) cc_final: 0.7066 (tmm) REVERT: B 184 LYS cc_start: 0.8366 (tttt) cc_final: 0.8072 (mttt) REVERT: C 53 ASN cc_start: 0.7555 (m-40) cc_final: 0.6589 (p0) REVERT: C 79 MET cc_start: 0.5599 (tpp) cc_final: 0.4546 (tpp) outliers start: 46 outliers final: 35 residues processed: 244 average time/residue: 0.1010 time to fit residues: 37.9711 Evaluate side-chains 241 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1530 VAL Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 61 optimal weight: 0.6980 chunk 139 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 127 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 941 GLN A1276 ASN A1686 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.243166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.201275 restraints weight = 32371.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202251 restraints weight = 42928.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.195988 restraints weight = 15075.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197152 restraints weight = 9859.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.197695 restraints weight = 7114.771| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15263 Z= 0.131 Angle : 0.576 10.127 20644 Z= 0.288 Chirality : 0.039 0.172 2323 Planarity : 0.004 0.093 2429 Dihedral : 11.562 145.566 2465 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.66 % Allowed : 19.56 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1703 helix: 1.26 (0.16), residues: 977 sheet: -1.29 (0.42), residues: 135 loop : -1.12 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 841 TYR 0.022 0.001 TYR A 81 PHE 0.014 0.001 PHE B 59 TRP 0.021 0.001 TRP A1408 HIS 0.002 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15241) covalent geometry : angle 0.56144 / 0.29 (20589) SS BOND : bond 0.00254 / 0.17 ( 11) SS BOND : angle 0.69142 / 0.49 ( 22) hydrogen bonds : bond 0.03618 / 2.33 ( 837) hydrogen bonds : angle 4.41527 / 3.13 ( 2367) link_BETA1-4 : bond 0.00707 / 0.39 ( 3) link_BETA1-4 : angle 3.71958 / 2.16 ( 9) link_NAG-ASN : bond 0.00257 / 0.16 ( 8) link_NAG-ASN : angle 3.02023 / 1.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7448 (mttp) cc_final: 0.6802 (mmtp) REVERT: A 185 ARG cc_start: 0.8267 (mmt90) cc_final: 0.8020 (mmt180) REVERT: A 216 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 243 LYS cc_start: 0.7966 (mttp) cc_final: 0.7351 (mptt) REVERT: A 379 MET cc_start: 0.7710 (ptm) cc_final: 0.7445 (ttt) REVERT: A 1384 ASN cc_start: 0.8804 (t0) cc_final: 0.8595 (t0) REVERT: A 1394 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 1545 GLU cc_start: 0.7203 (tt0) cc_final: 0.6985 (tt0) REVERT: A 1826 MET cc_start: 0.1971 (mpp) cc_final: 0.1580 (mpp) REVERT: A 1830 MET cc_start: 0.2747 (mtt) cc_final: 0.0313 (ttm) REVERT: B 91 VAL cc_start: 0.8911 (p) cc_final: 0.8689 (m) REVERT: B 152 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7822 (ttp-170) REVERT: B 154 MET cc_start: 0.7350 (tpp) cc_final: 0.6951 (tpp) REVERT: B 162 MET cc_start: 0.7611 (mmp) cc_final: 0.7248 (mmm) REVERT: B 163 MET cc_start: 0.7500 (tmm) cc_final: 0.7007 (tmm) REVERT: B 184 LYS cc_start: 0.8359 (tttt) cc_final: 0.8056 (mttt) REVERT: C 79 MET cc_start: 0.6092 (tpp) cc_final: 0.5243 (tpp) outliers start: 41 outliers final: 33 residues processed: 248 average time/residue: 0.0926 time to fit residues: 35.7330 Evaluate side-chains 247 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1623 LEU Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 941 GLN A1571 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.241855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.194934 restraints weight = 28542.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194810 restraints weight = 35204.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197430 restraints weight = 20042.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.198776 restraints weight = 10912.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.199825 restraints weight = 9630.239| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.4217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15263 Z= 0.154 Angle : 0.595 10.560 20644 Z= 0.297 Chirality : 0.040 0.165 2323 Planarity : 0.004 0.094 2429 Dihedral : 11.489 145.349 2463 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.79 % Allowed : 19.95 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1703 helix: 1.14 (0.16), residues: 991 sheet: -1.24 (0.42), residues: 135 loop : -1.21 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 841 TYR 0.023 0.001 TYR A 81 PHE 0.016 0.001 PHE C 63 TRP 0.019 0.001 TRP A1408 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (15241) covalent geometry : angle 0.58106 / 0.29 (20589) SS BOND : bond 0.00292 / 0.19 ( 11) SS BOND : angle 0.80304 / 0.59 ( 22) hydrogen bonds : bond 0.03660 / 2.36 ( 837) hydrogen bonds : angle 4.44176 / 3.14 ( 2367) link_BETA1-4 : bond 0.00660 / 0.36 ( 3) link_BETA1-4 : angle 3.72292 / 2.20 ( 9) link_NAG-ASN : bond 0.00250 / 0.16 ( 8) link_NAG-ASN : angle 2.97002 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7797 (mmt180) REVERT: A 216 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7448 (t80) REVERT: A 243 LYS cc_start: 0.7972 (mttp) cc_final: 0.7392 (mptt) REVERT: A 379 MET cc_start: 0.7727 (ptm) cc_final: 0.7433 (ttt) REVERT: A 1394 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 1545 GLU cc_start: 0.7205 (tt0) cc_final: 0.6959 (tt0) REVERT: A 1826 MET cc_start: 0.2605 (mpp) cc_final: 0.2193 (mpp) REVERT: A 1830 MET cc_start: 0.3180 (mtt) cc_final: 0.0753 (ttm) REVERT: B 91 VAL cc_start: 0.8891 (p) cc_final: 0.8679 (m) REVERT: B 152 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7834 (ttp-170) REVERT: B 154 MET cc_start: 0.7288 (tpp) cc_final: 0.6922 (tpp) REVERT: B 162 MET cc_start: 0.7542 (mmp) cc_final: 0.7240 (mmm) REVERT: B 184 LYS cc_start: 0.8372 (tttt) cc_final: 0.8073 (mttt) REVERT: C 79 MET cc_start: 0.5526 (tpp) cc_final: 0.4663 (tpp) outliers start: 43 outliers final: 36 residues processed: 238 average time/residue: 0.1022 time to fit residues: 37.5763 Evaluate side-chains 242 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 121 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 137 optimal weight: 40.0000 chunk 119 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 138 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 941 GLN A1571 HIS ** B 115 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 = 0.4683 r_free = 0.4683 target = 0.243739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.199859 restraints weight = 34826.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.204417 restraints weight = 46894.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.205099 restraints weight = 14075.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.205474 restraints weight = 8801.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.206170 restraints weight = 7691.853| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4279 r_free = 0.4279 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4279 r_free = 0.4279 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15263 Z= 0.123 Angle : 0.579 10.750 20644 Z= 0.291 Chirality : 0.039 0.170 2323 Planarity : 0.004 0.092 2429 Dihedral : 11.274 144.498 2463 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 20.53 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1703 helix: 1.23 (0.16), residues: 996 sheet: -1.05 (0.44), residues: 129 loop : -1.18 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 841 TYR 0.025 0.001 TYR A 81 PHE 0.018 0.001 PHE C 63 TRP 0.021 0.001 TRP A1408 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15241) covalent geometry : angle 0.56632 / 0.29 (20589) SS BOND : bond 0.00227 / 0.15 ( 11) SS BOND : angle 0.65408 / 0.47 ( 22) hydrogen bonds : bond 0.03582 / 2.31 ( 837) hydrogen bonds : angle 4.39063 / 3.11 ( 2367) link_BETA1-4 : bond 0.00654 / 0.36 ( 3) link_BETA1-4 : angle 3.59039 / 2.07 ( 9) link_NAG-ASN : bond 0.00252 / 0.15 ( 8) link_NAG-ASN : angle 2.82558 / 1.79 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3406 Ramachandran restraints generated. 1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6225 (ttt) cc_final: 0.5928 (tmm) REVERT: A 185 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7726 (mmt180) REVERT: A 216 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7429 (t80) REVERT: A 243 LYS cc_start: 0.8011 (mttp) cc_final: 0.7340 (mptt) REVERT: A 379 MET cc_start: 0.7694 (ptm) cc_final: 0.7430 (ttt) REVERT: A 1384 ASN cc_start: 0.8791 (t0) cc_final: 0.8564 (t0) REVERT: A 1394 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7975 (mt) REVERT: A 1545 GLU cc_start: 0.7143 (tt0) cc_final: 0.6915 (tt0) REVERT: A 1668 TYR cc_start: 0.8230 (m-80) cc_final: 0.7949 (m-80) REVERT: A 1732 ASN cc_start: 0.8037 (t0) cc_final: 0.7789 (t0) REVERT: A 1826 MET cc_start: 0.2675 (mpp) cc_final: 0.2304 (mpp) REVERT: A 1830 MET cc_start: 0.3197 (mtt) cc_final: 0.0839 (ttm) REVERT: B 91 VAL cc_start: 0.8856 (p) cc_final: 0.8651 (m) REVERT: B 152 ARG cc_start: 0.8081 (ttp-170) cc_final: 0.7805 (ttp-170) REVERT: B 154 MET cc_start: 0.7245 (tpp) cc_final: 0.6845 (tpp) REVERT: B 162 MET cc_start: 0.7496 (mmp) cc_final: 0.7214 (mmm) REVERT: B 184 LYS cc_start: 0.8333 (tttt) cc_final: 0.8037 (mttt) REVERT: C 79 MET cc_start: 0.5373 (tpp) cc_final: 0.4519 (tpp) outliers start: 32 outliers final: 28 residues processed: 239 average time/residue: 0.1005 time to fit residues: 37.2566 Evaluate side-chains 241 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1343 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1394 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1714 ASP Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 0.2980 chunk 158 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1571 HIS ** B 115 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 = 0.4682 r_free = 0.4682 target = 0.243604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.199178 restraints weight = 33421.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.204096 restraints weight = 45448.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.204968 restraints weight = 13436.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.204934 restraints weight = 8362.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.206238 restraints weight = 7000.162| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4288 r_free = 0.4288 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4288 r_free = 0.4288 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15263 Z= 0.125 Angle : 0.582 10.632 20644 Z= 0.292 Chirality : 0.039 0.166 2323 Planarity : 0.004 0.093 2429 Dihedral : 11.165 144.066 2463 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.34 % Allowed : 20.14 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1703 helix: 1.33 (0.16), residues: 982 sheet: -1.11 (0.42), residues: 134 loop : -0.97 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 841 TYR 0.025 0.001 TYR A 81 PHE 0.025 0.001 PHE A 183 TRP 0.022 0.001 TRP A1408 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15241) covalent geometry : angle 0.56964 / 0.29 (20589) SS BOND : bond 0.00215 / 0.14 ( 11) SS BOND : angle 0.65418 / 0.47 ( 22) hydrogen bonds : bond 0.03572 / 2.30 ( 837) hydrogen bonds : angle 4.37570 / 3.10 ( 2367) link_BETA1-4 : bond 0.00635 / 0.35 ( 3) link_BETA1-4 : angle 3.56701 / 2.06 ( 9) link_NAG-ASN : bond 0.00244 / 0.15 ( 8) link_NAG-ASN : angle 2.75370 / 1.74 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2438.72 seconds wall clock time: 42 minutes 57.79 seconds (2577.79 seconds total)