Starting phenix.real_space_refine on Fri Jul 3 19:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9p_32371/07_2026/7w9p_32371.map" } resolution = 2.9 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= 0.008 sd= 0.120 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 9781 2.51 5 N 2232 2.21 5 O 2677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s 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: 14817 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1413, 11367 Classifications: {'peptide': 1413} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1362} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 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: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 911 Unusual residues: {'1PW': 1, '9SL': 1, 'LPE': 12, 'NAG': 2, 'PCW': 5, 'Y01': 6} Classifications: {'peptide': 3, 'undetermined': 27} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'P5S:plan-2': 1, '1PW:plan-1': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 16 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: 3.27, per 1000 atoms: 0.22 Number of scatterers: 14817 At special positions: 0 Unit cell: (129.829, 139.648, 142.921, 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 2677 8.00 N 2232 7.00 C 9781 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=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.14 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 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=2.04 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=1, 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 A2002 " - " 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 657.4 milliseconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 11 sheets defined 65.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.591A pdb=" N TYR A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 143 removed outlier: 3.723A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.641A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 246 through 267 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.072A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.788A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 428 removed outlier: 3.590A pdb=" N ASN A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 806 removed outlier: 3.944A pdb=" N VAL A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 824 Processing helix chain 'A' and resid 831 through 844 removed outlier: 3.562A pdb=" N ARG A 835 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 840 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 864 Processing helix chain 'A' and resid 866 through 895 removed outlier: 4.355A pdb=" N THR A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 872 " --> pdb=" O ASN A 868 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.520A pdb=" N VAL A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 removed outlier: 3.829A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 removed outlier: 4.024A pdb=" N LEU A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1211 removed outlier: 3.731A pdb=" N GLU A1195 " --> pdb=" O HIS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1248 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1257 through 1278 Processing helix chain 'A' and resid 1285 through 1290 Processing helix chain 'A' and resid 1291 through 1298 removed outlier: 3.624A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 4.009A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1343 removed outlier: 4.001A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.768A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A1326 " --> pdb=" O MET A1322 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A1327 " --> pdb=" O ASN A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.544A pdb=" N CYS A1370 " --> pdb=" O ASN A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 removed outlier: 3.576A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 4.084A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) 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 1444 removed outlier: 3.825A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1467 removed outlier: 3.610A pdb=" N LYS A1465 " --> pdb=" O ASN A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 4.022A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 removed outlier: 3.602A pdb=" N CYS A1507 " --> pdb=" O LYS A1503 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN A1514 " --> pdb=" O ASP A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1533 removed outlier: 3.622A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A1526 " --> pdb=" O MET A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.632A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1603 removed outlier: 3.512A pdb=" N PHE A1581 " --> pdb=" O GLY A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1617 through 1622 removed outlier: 4.017A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1626 removed outlier: 3.859A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1623 through 1626' Processing helix chain 'A' and resid 1628 through 1639 Processing helix chain 'A' and resid 1640 through 1664 removed outlier: 3.559A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1695 Processing helix chain 'A' and resid 1699 through 1705 removed outlier: 3.587A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1708 No H-bonds generated for 'chain 'A' and resid 1706 through 1708' Processing helix chain 'A' and resid 1732 through 1768 removed outlier: 3.882A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1790 removed outlier: 3.514A pdb=" N PHE A1779 " --> pdb=" O SER A1775 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A1788 " --> pdb=" O GLU A1784 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 3.597A pdb=" N SER A1803 " --> pdb=" O PHE A1799 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1826 removed outlier: 3.594A pdb=" N ILE A1824 " --> pdb=" O LYS A1820 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA A1825 " --> pdb=" O VAL A1821 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A1826 " --> pdb=" O GLN A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1851 removed outlier: 3.843A pdb=" N ARG A1848 " --> pdb=" O ALA A1844 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A1849 " --> pdb=" O PHE A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1871 removed outlier: 4.248A pdb=" N ASP A1857 " --> pdb=" O SER A1853 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1858 " --> pdb=" O GLY A1854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.598A pdb=" N SER A1876 " --> pdb=" O SER A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1891 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 191 removed outlier: 3.920A pdb=" N ILE B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (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 87 through 91 removed outlier: 3.514A pdb=" N PHE A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 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: 6.615A 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: 6.126A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 68 " --> pdb=" O PHE B 59 " (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 126 through 128 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: 7.276A 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: 6.354A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.486A 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 48 831 hydrogen bonds defined for protein. 2379 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: 2.97 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2231 1.29 - 1.43: 3997 1.43 - 1.57: 8681 1.57 - 1.71: 59 1.71 - 1.85: 172 Bond restraints: 15140 Sorted by residual: bond pdb=" C12 9SL A2001 " pdb=" N11 9SL A2001 " ideal model delta sigma weight residual 1.284 1.504 -0.220 2.00e-02 2.50e+03 1.21e+02 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 9.87e+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 1.455 -0.129 2.00e-02 2.50e+03 4.19e+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 4.04e+01 ... (remaining 15135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 20316 6.76 - 13.53: 132 13.53 - 20.29: 0 20.29 - 27.05: 0 27.05 - 33.82: 3 Bond angle restraints: 20451 Sorted by residual: angle pdb=" C5 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 111.64 77.82 33.82 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C6 PCW A2028 " pdb=" N PCW A2028 " pdb=" C8 PCW A2028 " ideal model delta sigma weight residual 109.11 78.00 31.11 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 78.15 30.09 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N LYS A1670 " pdb=" CA LYS A1670 " pdb=" C LYS A1670 " ideal model delta sigma weight residual 111.71 122.19 -10.48 1.15e+00 7.56e-01 8.30e+01 angle pdb=" N ALA A1344 " pdb=" CA ALA A1344 " pdb=" C ALA A1344 " ideal model delta sigma weight residual 111.14 119.69 -8.55 1.08e+00 8.57e-01 6.26e+01 ... (remaining 20446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 8588 32.10 - 64.21: 369 64.21 - 96.31: 38 96.31 - 128.41: 11 128.41 - 160.52: 1 Dihedral angle restraints: 9007 sinusoidal: 3986 harmonic: 5021 Sorted by residual: dihedral pdb=" CB CYS A 895 " pdb=" SG CYS A 895 " pdb=" SG CYS C 55 " pdb=" CB CYS C 55 " ideal model delta sinusoidal sigma weight residual 93.00 146.84 -53.84 1 1.00e+01 1.00e-02 3.94e+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 93.00 142.29 -49.29 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS A 897 " pdb=" SG CYS A 897 " pdb=" SG CYS A 903 " pdb=" CB CYS A 903 " ideal model delta sinusoidal sigma weight residual 93.00 132.88 -39.88 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 9004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2181 0.143 - 0.286: 94 0.286 - 0.430: 20 0.430 - 0.573: 8 0.573 - 0.716: 1 Chirality restraints: 2304 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 -1.68 -0.72 2.00e-02 2.50e+03 1.28e+03 chirality pdb=" CBG Y01 A2005 " pdb=" CAQ Y01 A2005 " pdb=" CBD Y01 A2005 " pdb=" CBI Y01 A2005 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CBG Y01 A2006 " pdb=" CAQ Y01 A2006 " pdb=" CBD Y01 A2006 " pdb=" CBI Y01 A2006 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.23e+00 ... (remaining 2301 not shown) Planarity restraints: 2428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1375 " 0.087 2.00e-02 2.50e+03 3.61e-01 1.63e+03 pdb=" CG ASN A1375 " -0.098 2.00e-02 2.50e+03 pdb=" OD1 ASN A1375 " 0.225 2.00e-02 2.50e+03 pdb=" ND2 ASN A1375 " -0.637 2.00e-02 2.50e+03 pdb=" C1 NAG A2008 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2008 " 0.203 2.00e-02 2.50e+03 1.68e-01 3.54e+02 pdb=" C7 NAG A2008 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG A2008 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG A2008 " -0.276 2.00e-02 2.50e+03 pdb=" O7 NAG A2008 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1366 " -0.136 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN A1366 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A1366 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A1366 " 0.236 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.175 2.00e-02 2.50e+03 ... (remaining 2425 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 80 2.49 - 3.10: 11373 3.10 - 3.70: 21767 3.70 - 4.30: 32672 4.30 - 4.90: 52860 Nonbonded interactions: 118752 Sorted by model distance: nonbonded pdb=" OD2 ASP A1355 " pdb=" O5 NAG D 1 " model vdw 1.893 3.040 nonbonded pdb=" CD1 PHE A 843 " pdb=" CD1 LEU A 852 " model vdw 1.920 3.760 nonbonded pdb=" OD1 ASP A1355 " pdb=" C6 NAG D 1 " model vdw 1.936 3.440 nonbonded pdb=" CD2 LEU A 53 " pdb=" CB ASP A 79 " model vdw 1.960 3.860 nonbonded pdb=" O SER A 862 " pdb=" O LEU A 866 " model vdw 2.052 3.040 ... (remaining 118747 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 : 0.014 0.601 15163 Z= 0.830 Angle : 1.524 60.697 20506 Z= 0.719 Chirality : 0.077 0.716 2304 Planarity : 0.006 0.168 2420 Dihedral : 17.297 160.515 5726 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.43 % Favored : 95.27 % Rotamer: Outliers : 2.81 % Allowed : 11.06 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.18), residues: 1696 helix: -0.84 (0.15), residues: 981 sheet: -1.80 (0.40), residues: 140 loop : -2.22 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 115 TYR 0.033 0.002 TYR A1413 PHE 0.030 0.002 PHE B 54 TRP 0.051 0.002 TRP A 933 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.01274 / 0.66 (15140) covalent geometry : angle 1.38043 / 0.68 (20451) SS BOND : bond 0.03543 / 1.85 ( 11) SS BOND : angle 9.06680 / 4.07 ( 22) hydrogen bonds : bond 0.18188 / 11.97 ( 831) hydrogen bonds : angle 7.11622 / 5.08 ( 2379) Misc. bond : bond 0.60117 / 37.57 ( 1) link_BETA1-4 : bond 0.04550 / 2.53 ( 3) link_BETA1-4 : angle 21.01551 / 15.32 ( 9) link_NAG-ASN : bond 0.10393 / 7.22 ( 8) link_NAG-ASN : angle 10.89359 / 8.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7106 (tp) REVERT: A 133 MET cc_start: 0.7210 (ttp) cc_final: 0.6986 (ttp) REVERT: A 181 PHE cc_start: 0.7086 (m-80) cc_final: 0.6771 (m-80) REVERT: A 216 PHE cc_start: 0.8252 (m-80) cc_final: 0.7909 (m-80) REVERT: A 249 MET cc_start: 0.7843 (mmm) cc_final: 0.7621 (mmt) REVERT: A 310 LYS cc_start: 0.8322 (mttt) cc_final: 0.8010 (mtmt) REVERT: A 810 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6861 (tp) REVERT: A 890 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7340 (tptt) REVERT: A 894 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 932 MET cc_start: 0.8904 (ttp) cc_final: 0.8622 (ttm) REVERT: A 961 ASN cc_start: 0.8104 (t0) cc_final: 0.7550 (m-40) REVERT: A 1212 GLU cc_start: 0.7719 (tt0) cc_final: 0.6509 (pp20) REVERT: A 1282 ASP cc_start: 0.6661 (t0) cc_final: 0.6265 (t0) REVERT: A 1449 LEU cc_start: 0.6617 (mm) cc_final: 0.6335 (mm) REVERT: A 1543 MET cc_start: 0.8078 (ttp) cc_final: 0.7554 (tpt) REVERT: A 1639 MET cc_start: 0.8749 (mmp) cc_final: 0.8461 (mmp) REVERT: A 1774 LEU cc_start: 0.0042 (OUTLIER) cc_final: -0.0342 (mt) REVERT: A 1826 MET cc_start: -0.0673 (mtm) cc_final: -0.1359 (mpp) REVERT: A 1830 MET cc_start: -0.0082 (mmt) cc_final: -0.1168 (ppp) REVERT: B 118 ASP cc_start: 0.8245 (m-30) cc_final: 0.7994 (m-30) REVERT: B 141 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8245 (mttp) REVERT: B 163 MET cc_start: 0.8355 (tmt) cc_final: 0.7793 (tmm) REVERT: B 164 TYR cc_start: 0.8281 (m-80) cc_final: 0.7922 (m-10) outliers start: 43 outliers final: 11 residues processed: 290 average time/residue: 0.5466 time to fit residues: 175.9884 Evaluate side-chains 203 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1774 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 282 ASN A 360 GLN A 395 ASN A 780 ASN A 868 ASN A 886 GLN A 909 HIS A 911 ASN A 941 GLN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN ** A1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1459 ASN A1461 ASN A1478 GLN A1528 ASN ** A1539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1541 GLN A1571 HIS A1795 GLN B 102 GLN B 143 HIS B 151 ASN C 53 ASN C 82 GLN C 89 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108766 restraints weight = 46785.312| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.53 r_work: 0.3064 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15163 Z= 0.144 Angle : 0.682 14.315 20506 Z= 0.333 Chirality : 0.046 0.596 2304 Planarity : 0.004 0.044 2420 Dihedral : 15.754 164.151 2464 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.34 % Allowed : 15.84 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1696 helix: 0.84 (0.16), residues: 981 sheet: -1.44 (0.40), residues: 139 loop : -1.58 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 994 TYR 0.017 0.002 TYR A1602 PHE 0.033 0.002 PHE A 88 TRP 0.027 0.001 TRP A 933 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15140) covalent geometry : angle 0.65594 / 0.33 (20451) SS BOND : bond 0.00414 / 0.29 ( 11) SS BOND : angle 1.97346 / 1.45 ( 22) hydrogen bonds : bond 0.05714 / 3.72 ( 831) hydrogen bonds : angle 4.88481 / 3.46 ( 2379) Misc. bond : bond 0.00276 / 0.17 ( 1) link_BETA1-4 : bond 0.00638 / 0.39 ( 3) link_BETA1-4 : angle 4.17398 / 3.10 ( 9) link_NAG-ASN : bond 0.01534 / 1.19 ( 8) link_NAG-ASN : angle 4.49645 / 3.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PHE cc_start: 0.7753 (m-80) cc_final: 0.7517 (m-80) REVERT: A 200 TYR cc_start: 0.6784 (m-80) cc_final: 0.6579 (m-80) REVERT: A 287 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 310 LYS cc_start: 0.8789 (mttt) cc_final: 0.8516 (mtmt) REVERT: A 810 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6913 (tp) REVERT: A 890 LYS cc_start: 0.8595 (mtpp) cc_final: 0.7948 (tptt) REVERT: A 894 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 961 ASN cc_start: 0.8292 (t0) cc_final: 0.7864 (m-40) REVERT: A 994 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7169 (tpt90) REVERT: A 1212 GLU cc_start: 0.8031 (tt0) cc_final: 0.6784 (pp20) REVERT: A 1323 ASN cc_start: 0.8849 (t0) cc_final: 0.8595 (t0) REVERT: A 1378 GLN cc_start: 0.8629 (mt0) cc_final: 0.8378 (tt0) REVERT: A 1449 LEU cc_start: 0.7077 (mm) cc_final: 0.6824 (mm) REVERT: A 1462 GLN cc_start: 0.8542 (tp40) cc_final: 0.7966 (tt0) REVERT: A 1543 MET cc_start: 0.8575 (ttp) cc_final: 0.7910 (tpt) REVERT: A 1565 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6926 (mtpt) REVERT: A 1787 GLU cc_start: 0.1585 (OUTLIER) cc_final: 0.1256 (tp30) REVERT: A 1826 MET cc_start: -0.1935 (mtm) cc_final: -0.2535 (mpp) REVERT: B 141 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8399 (mttp) REVERT: B 163 MET cc_start: 0.8422 (tmt) cc_final: 0.8079 (tmm) REVERT: B 164 TYR cc_start: 0.8165 (m-80) cc_final: 0.7947 (m-10) REVERT: C 52 PHE cc_start: 0.5217 (p90) cc_final: 0.4970 (p90) outliers start: 51 outliers final: 15 residues processed: 250 average time/residue: 0.5448 time to fit residues: 152.0041 Evaluate side-chains 197 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 1218 ARG Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1565 LYS Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 7 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 139 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS B 61 GLN C 39 ASN C 59 ASN C 89 ASN C 118 GLN C 143 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.177551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108017 restraints weight = 25372.551| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.73 r_work: 0.3130 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15163 Z= 0.141 Angle : 0.612 13.937 20506 Z= 0.301 Chirality : 0.043 0.433 2304 Planarity : 0.004 0.039 2420 Dihedral : 14.537 160.058 2447 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.19 % Allowed : 18.32 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1696 helix: 1.29 (0.16), residues: 985 sheet: -1.44 (0.38), residues: 143 loop : -1.35 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 994 TYR 0.017 0.001 TYR A1602 PHE 0.033 0.002 PHE A 843 TRP 0.019 0.001 TRP A 933 HIS 0.004 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15140) covalent geometry : angle 0.59100 / 0.30 (20451) SS BOND : bond 0.00385 / 0.24 ( 11) SS BOND : angle 1.05968 / 0.72 ( 22) hydrogen bonds : bond 0.04958 / 3.25 ( 831) hydrogen bonds : angle 4.59287 / 3.26 ( 2379) Misc. bond : bond 0.00056 / 0.03 ( 1) link_BETA1-4 : bond 0.00573 / 0.34 ( 3) link_BETA1-4 : angle 3.40278 / 2.48 ( 9) link_NAG-ASN : bond 0.00794 / 0.57 ( 8) link_NAG-ASN : angle 4.07412 / 2.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4135 (mtt) cc_final: 0.3848 (mtp) REVERT: A 200 TYR cc_start: 0.6982 (m-80) cc_final: 0.6645 (m-80) REVERT: A 287 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7363 (mp0) REVERT: A 310 LYS cc_start: 0.8821 (mttt) cc_final: 0.8518 (mtmm) REVERT: A 388 LEU cc_start: 0.8227 (mp) cc_final: 0.7594 (tp) REVERT: A 768 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8238 (tpp) REVERT: A 791 MET cc_start: 0.6416 (ttp) cc_final: 0.6114 (ttm) REVERT: A 890 LYS cc_start: 0.8668 (mtpp) cc_final: 0.7932 (tptt) REVERT: A 894 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 961 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: A 994 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7208 (tpt90) REVERT: A 1212 GLU cc_start: 0.7992 (tt0) cc_final: 0.6759 (pp20) REVERT: A 1239 LEU cc_start: 0.8747 (mt) cc_final: 0.8531 (tp) REVERT: A 1282 ASP cc_start: 0.7156 (t0) cc_final: 0.6663 (t0) REVERT: A 1287 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8635 (mppt) REVERT: A 1378 GLN cc_start: 0.8588 (mt0) cc_final: 0.8344 (tt0) REVERT: A 1449 LEU cc_start: 0.7079 (mm) cc_final: 0.6765 (tp) REVERT: A 1487 LYS cc_start: 0.7332 (tmmt) cc_final: 0.7068 (ttpp) REVERT: A 1543 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8016 (tpt) REVERT: A 1561 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: A 1762 ASN cc_start: 0.8570 (m-40) cc_final: 0.8194 (m-40) REVERT: A 1787 GLU cc_start: 0.1789 (OUTLIER) cc_final: 0.1375 (tp30) REVERT: A 1797 ILE cc_start: -0.0878 (OUTLIER) cc_final: -0.1415 (pt) REVERT: A 1826 MET cc_start: -0.1880 (mtm) cc_final: -0.2525 (mpp) REVERT: A 1830 MET cc_start: -0.1515 (tpt) cc_final: -0.2076 (ppp) REVERT: B 76 GLU cc_start: 0.8475 (mp0) cc_final: 0.7994 (mp0) REVERT: B 141 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8475 (mttp) REVERT: B 163 MET cc_start: 0.8450 (tmt) cc_final: 0.8215 (tmm) REVERT: B 164 TYR cc_start: 0.8220 (m-80) cc_final: 0.7985 (m-10) REVERT: B 170 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7569 (mp) REVERT: C 52 PHE cc_start: 0.5350 (p90) cc_final: 0.4975 (p90) REVERT: C 104 ASN cc_start: -0.0895 (t0) cc_final: -0.1392 (p0) outliers start: 64 outliers final: 28 residues processed: 239 average time/residue: 0.5400 time to fit residues: 143.7133 Evaluate side-chains 213 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1218 ARG Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS A1732 ASN C 39 ASN C 53 ASN C 59 ASN C 89 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.174558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103434 restraints weight = 34214.722| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.14 r_work: 0.3054 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15163 Z= 0.224 Angle : 0.677 13.874 20506 Z= 0.331 Chirality : 0.045 0.419 2304 Planarity : 0.004 0.058 2420 Dihedral : 14.246 156.467 2445 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.65 % Allowed : 19.83 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1696 helix: 1.25 (0.16), residues: 983 sheet: -1.33 (0.39), residues: 143 loop : -1.35 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1218 TYR 0.019 0.002 TYR A1602 PHE 0.035 0.002 PHE A 843 TRP 0.013 0.001 TRP A 849 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (15140) covalent geometry : angle 0.65728 / 0.33 (20451) SS BOND : bond 0.00476 / 0.35 ( 11) SS BOND : angle 1.40228 / 0.91 ( 22) hydrogen bonds : bond 0.05514 / 3.61 ( 831) hydrogen bonds : angle 4.65541 / 3.31 ( 2379) Misc. bond : bond 0.00049 / 0.03 ( 1) link_BETA1-4 : bond 0.00462 / 0.28 ( 3) link_BETA1-4 : angle 3.48595 / 2.52 ( 9) link_NAG-ASN : bond 0.00734 / 0.52 ( 8) link_NAG-ASN : angle 4.08180 / 2.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4754 (mtt) cc_final: 0.4509 (mtp) REVERT: A 99 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7410 (mtp180) REVERT: A 200 TYR cc_start: 0.7074 (m-80) cc_final: 0.6767 (m-80) REVERT: A 307 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: A 310 LYS cc_start: 0.8790 (mttt) cc_final: 0.8522 (mtmt) REVERT: A 364 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: A 388 LEU cc_start: 0.8141 (mp) cc_final: 0.7582 (tp) REVERT: A 768 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7915 (ttp) REVERT: A 798 MET cc_start: 0.6598 (ptt) cc_final: 0.5757 (pmt) REVERT: A 843 PHE cc_start: 0.6547 (m-10) cc_final: 0.6287 (m-80) REVERT: A 854 MET cc_start: 0.6098 (mpt) cc_final: 0.5702 (mpt) REVERT: A 890 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7883 (tptt) REVERT: A 894 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 961 ASN cc_start: 0.8245 (t0) cc_final: 0.8021 (m110) REVERT: A 994 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7191 (tpt90) REVERT: A 1212 GLU cc_start: 0.7896 (tt0) cc_final: 0.6742 (pp20) REVERT: A 1282 ASP cc_start: 0.7210 (t0) cc_final: 0.6990 (t0) REVERT: A 1287 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8315 (mppt) REVERT: A 1328 CYS cc_start: 0.8446 (m) cc_final: 0.8138 (m) REVERT: A 1449 LEU cc_start: 0.7295 (mm) cc_final: 0.7010 (tp) REVERT: A 1462 GLN cc_start: 0.8500 (tp40) cc_final: 0.7984 (tt0) REVERT: A 1543 MET cc_start: 0.8489 (ttp) cc_final: 0.7970 (tpt) REVERT: A 1561 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: A 1565 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6738 (mtpt) REVERT: A 1588 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 1688 MET cc_start: 0.8978 (mmm) cc_final: 0.8750 (mmm) REVERT: A 1762 ASN cc_start: 0.8531 (m-40) cc_final: 0.8116 (m-40) REVERT: A 1787 GLU cc_start: 0.1859 (OUTLIER) cc_final: 0.1448 (tp30) REVERT: A 1797 ILE cc_start: -0.0902 (OUTLIER) cc_final: -0.1247 (pt) REVERT: A 1826 MET cc_start: -0.1928 (mtm) cc_final: -0.2607 (mpp) REVERT: A 1856 MET cc_start: -0.1558 (tpt) cc_final: -0.1918 (ptp) REVERT: B 27 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8410 (mt-10) REVERT: B 76 GLU cc_start: 0.8289 (mp0) cc_final: 0.7837 (mp0) REVERT: B 141 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8422 (mtmt) REVERT: B 163 MET cc_start: 0.8413 (tmt) cc_final: 0.8165 (tmm) REVERT: B 164 TYR cc_start: 0.8234 (m-80) cc_final: 0.8013 (m-80) REVERT: B 170 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 52 PHE cc_start: 0.5525 (p90) cc_final: 0.5251 (p90) outliers start: 71 outliers final: 29 residues processed: 236 average time/residue: 0.5291 time to fit residues: 138.7580 Evaluate side-chains 207 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1218 ARG Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1565 LYS Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1767 THR Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS A 774 ASN A 961 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS C 39 ASN C 53 ASN C 59 ASN C 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107560 restraints weight = 47785.645| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.29 r_work: 0.3061 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15163 Z= 0.114 Angle : 0.574 13.862 20506 Z= 0.280 Chirality : 0.041 0.401 2304 Planarity : 0.004 0.053 2420 Dihedral : 13.429 157.023 2445 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.53 % Allowed : 20.94 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1696 helix: 1.61 (0.16), residues: 984 sheet: -1.20 (0.38), residues: 143 loop : -1.09 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.019 0.001 TYR A1602 PHE 0.037 0.001 PHE A 88 TRP 0.011 0.001 TRP A 190 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15140) covalent geometry : angle 0.55372 / 0.28 (20451) SS BOND : bond 0.00267 / 0.18 ( 11) SS BOND : angle 0.93919 / 0.60 ( 22) hydrogen bonds : bond 0.04317 / 2.82 ( 831) hydrogen bonds : angle 4.35603 / 3.10 ( 2379) Misc. bond : bond 0.00033 / 0.02 ( 1) link_BETA1-4 : bond 0.00395 / 0.23 ( 3) link_BETA1-4 : angle 3.04999 / 2.33 ( 9) link_NAG-ASN : bond 0.00758 / 0.55 ( 8) link_NAG-ASN : angle 3.95744 / 2.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7235 (m-80) cc_final: 0.6903 (m-80) REVERT: A 287 GLU cc_start: 0.7552 (mp0) cc_final: 0.7116 (mp0) REVERT: A 310 LYS cc_start: 0.8830 (mttt) cc_final: 0.8531 (mtmm) REVERT: A 364 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: A 388 LEU cc_start: 0.8098 (mp) cc_final: 0.7546 (tp) REVERT: A 426 MET cc_start: 0.2596 (tpt) cc_final: 0.1722 (ppp) REVERT: A 733 PHE cc_start: 0.5052 (OUTLIER) cc_final: 0.4721 (m-80) REVERT: A 768 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: A 791 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.6093 (ttm) REVERT: A 798 MET cc_start: 0.6695 (ptt) cc_final: 0.6037 (pmt) REVERT: A 854 MET cc_start: 0.5964 (mpt) cc_final: 0.5547 (mpt) REVERT: A 890 LYS cc_start: 0.8546 (mtpp) cc_final: 0.7929 (tptt) REVERT: A 894 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 961 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7888 (m-40) REVERT: A 994 ARG cc_start: 0.7517 (mtp85) cc_final: 0.7277 (tpt90) REVERT: A 1239 LEU cc_start: 0.8736 (mt) cc_final: 0.8533 (tp) REVERT: A 1282 ASP cc_start: 0.7131 (t0) cc_final: 0.6912 (t0) REVERT: A 1287 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8292 (mppt) REVERT: A 1378 GLN cc_start: 0.8674 (tt0) cc_final: 0.8362 (tt0) REVERT: A 1449 LEU cc_start: 0.7268 (mm) cc_final: 0.6981 (tp) REVERT: A 1462 GLN cc_start: 0.8559 (tp40) cc_final: 0.7951 (tt0) REVERT: A 1515 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6238 (mm110) REVERT: A 1543 MET cc_start: 0.8475 (ttp) cc_final: 0.7990 (tpt) REVERT: A 1561 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: A 1565 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6924 (mtmt) REVERT: A 1762 ASN cc_start: 0.8450 (m-40) cc_final: 0.8084 (m-40) REVERT: A 1787 GLU cc_start: 0.1987 (OUTLIER) cc_final: 0.1552 (tp30) REVERT: A 1797 ILE cc_start: -0.0776 (OUTLIER) cc_final: -0.1173 (pt) REVERT: A 1826 MET cc_start: -0.2160 (mtm) cc_final: -0.2718 (mpp) REVERT: B 27 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8418 (mt-10) REVERT: B 141 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8484 (mtmt) REVERT: B 164 TYR cc_start: 0.8167 (m-80) cc_final: 0.7928 (m-80) REVERT: B 170 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 52 PHE cc_start: 0.5534 (p90) cc_final: 0.5219 (p90) REVERT: C 79 MET cc_start: 0.4400 (tpt) cc_final: 0.4128 (tpp) outliers start: 54 outliers final: 21 residues processed: 219 average time/residue: 0.5448 time to fit residues: 132.7684 Evaluate side-chains 200 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1218 ARG Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1515 GLN Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1565 LYS Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 27 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 131 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN A 809 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS C 39 ASN C 53 ASN C 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.175891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106555 restraints weight = 34511.714| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.87 r_work: 0.3061 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15163 Z= 0.163 Angle : 0.611 13.827 20506 Z= 0.299 Chirality : 0.043 0.408 2304 Planarity : 0.004 0.054 2420 Dihedral : 13.213 155.667 2445 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.12 % Allowed : 21.14 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.75 (0.20), residues: 1696 helix: 1.67 (0.16), residues: 984 sheet: -1.11 (0.38), residues: 144 loop : -1.15 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.017 0.001 TYR A1602 PHE 0.040 0.002 PHE A 843 TRP 0.009 0.001 TRP A 190 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (15140) covalent geometry : angle 0.58821 / 0.29 (20451) SS BOND : bond 0.00614 / 0.45 ( 11) SS BOND : angle 2.28714 / 1.62 ( 22) hydrogen bonds : bond 0.04696 / 3.06 ( 831) hydrogen bonds : angle 4.36991 / 3.12 ( 2379) Misc. bond : bond 0.00045 / 0.03 ( 1) link_BETA1-4 : bond 0.00357 / 0.22 ( 3) link_BETA1-4 : angle 2.98957 / 2.24 ( 9) link_NAG-ASN : bond 0.00727 / 0.53 ( 8) link_NAG-ASN : angle 3.97723 / 2.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7079 (m-80) cc_final: 0.6775 (m-80) REVERT: A 310 LYS cc_start: 0.8816 (mttt) cc_final: 0.8512 (mtmm) REVERT: A 364 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8827 (pm20) REVERT: A 388 LEU cc_start: 0.8104 (mp) cc_final: 0.7522 (tp) REVERT: A 426 MET cc_start: 0.2716 (tpt) cc_final: 0.1768 (ppp) REVERT: A 733 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4808 (m-80) REVERT: A 798 MET cc_start: 0.6688 (ptt) cc_final: 0.5918 (pmt) REVERT: A 890 LYS cc_start: 0.8547 (mtpp) cc_final: 0.7877 (tptt) REVERT: A 894 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 961 ASN cc_start: 0.8514 (t0) cc_final: 0.8145 (t160) REVERT: A 994 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7261 (tpt90) REVERT: A 1239 LEU cc_start: 0.8734 (mt) cc_final: 0.8514 (tp) REVERT: A 1282 ASP cc_start: 0.7192 (t0) cc_final: 0.6929 (t0) REVERT: A 1287 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8403 (mptt) REVERT: A 1378 GLN cc_start: 0.8656 (tt0) cc_final: 0.8325 (tt0) REVERT: A 1449 LEU cc_start: 0.7416 (mm) cc_final: 0.7121 (tp) REVERT: A 1543 MET cc_start: 0.8428 (ttp) cc_final: 0.7946 (tpt) REVERT: A 1561 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 1565 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6699 (mtpt) REVERT: A 1762 ASN cc_start: 0.8464 (m-40) cc_final: 0.8044 (m-40) REVERT: A 1787 GLU cc_start: 0.1881 (OUTLIER) cc_final: 0.1466 (tp30) REVERT: A 1797 ILE cc_start: -0.0722 (OUTLIER) cc_final: -0.1109 (pt) REVERT: A 1826 MET cc_start: -0.2064 (mtm) cc_final: -0.2649 (mpp) REVERT: B 27 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8433 (mt-10) REVERT: B 141 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8465 (mtmt) REVERT: B 170 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7507 (mp) REVERT: C 52 PHE cc_start: 0.5691 (p90) cc_final: 0.5432 (p90) REVERT: C 79 MET cc_start: 0.4449 (tpt) cc_final: 0.4190 (tpp) outliers start: 63 outliers final: 29 residues processed: 221 average time/residue: 0.5221 time to fit residues: 129.0299 Evaluate side-chains 209 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1218 ARG Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1565 LYS Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN A 956 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS C 39 ASN C 53 ASN C 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107527 restraints weight = 32962.665| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.20 r_work: 0.3116 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15163 Z= 0.112 Angle : 0.563 13.921 20506 Z= 0.278 Chirality : 0.041 0.397 2304 Planarity : 0.004 0.056 2420 Dihedral : 12.578 155.835 2445 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.32 % Allowed : 21.07 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.97 (0.21), residues: 1696 helix: 1.82 (0.16), residues: 990 sheet: -0.95 (0.39), residues: 144 loop : -1.04 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.020 0.001 TYR A1602 PHE 0.053 0.001 PHE A 843 TRP 0.013 0.001 TRP A 190 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15140) covalent geometry : angle 0.54252 / 0.27 (20451) SS BOND : bond 0.00422 / 0.34 ( 11) SS BOND : angle 1.25226 / 0.87 ( 22) hydrogen bonds : bond 0.04078 / 2.65 ( 831) hydrogen bonds : angle 4.24026 / 3.02 ( 2379) Misc. bond : bond 0.00034 / 0.02 ( 1) link_BETA1-4 : bond 0.00322 / 0.18 ( 3) link_BETA1-4 : angle 2.84627 / 2.21 ( 9) link_NAG-ASN : bond 0.00777 / 0.57 ( 8) link_NAG-ASN : angle 3.93401 / 2.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6008 (t0) REVERT: A 156 GLU cc_start: 0.8036 (pp20) cc_final: 0.7762 (pp20) REVERT: A 157 TYR cc_start: 0.8558 (m-10) cc_final: 0.8330 (m-10) REVERT: A 181 PHE cc_start: 0.7444 (m-80) cc_final: 0.7204 (m-10) REVERT: A 200 TYR cc_start: 0.7203 (m-80) cc_final: 0.6852 (m-80) REVERT: A 287 GLU cc_start: 0.7501 (mp0) cc_final: 0.7071 (mp0) REVERT: A 310 LYS cc_start: 0.8795 (mttt) cc_final: 0.8513 (mtmm) REVERT: A 364 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: A 426 MET cc_start: 0.2878 (tpt) cc_final: 0.1998 (ppp) REVERT: A 733 PHE cc_start: 0.5133 (OUTLIER) cc_final: 0.4819 (m-80) REVERT: A 798 MET cc_start: 0.6719 (ptt) cc_final: 0.5993 (pmt) REVERT: A 890 LYS cc_start: 0.8482 (mtpp) cc_final: 0.7903 (tptt) REVERT: A 894 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7457 (mt-10) REVERT: A 961 ASN cc_start: 0.8372 (t0) cc_final: 0.7949 (m-40) REVERT: A 1322 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8062 (mmm) REVERT: A 1374 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7925 (mtt) REVERT: A 1378 GLN cc_start: 0.8663 (tt0) cc_final: 0.8403 (tt0) REVERT: A 1449 LEU cc_start: 0.7335 (mm) cc_final: 0.7009 (tp) REVERT: A 1462 GLN cc_start: 0.8493 (tp40) cc_final: 0.7866 (tt0) REVERT: A 1543 MET cc_start: 0.8354 (ttp) cc_final: 0.7902 (tpt) REVERT: A 1561 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: A 1565 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6805 (mtmt) REVERT: A 1762 ASN cc_start: 0.8306 (m-40) cc_final: 0.7923 (m-40) REVERT: A 1787 GLU cc_start: 0.1807 (OUTLIER) cc_final: 0.1454 (tp30) REVERT: A 1797 ILE cc_start: -0.0900 (OUTLIER) cc_final: -0.1221 (pt) REVERT: A 1826 MET cc_start: -0.1865 (mtm) cc_final: -0.2550 (mpp) REVERT: B 27 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8317 (mt-10) REVERT: B 28 THR cc_start: 0.8734 (p) cc_final: 0.8493 (m) REVERT: B 141 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8461 (mtmt) REVERT: B 170 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7612 (mp) REVERT: C 52 PHE cc_start: 0.5665 (p90) cc_final: 0.5390 (p90) REVERT: C 79 MET cc_start: 0.4411 (tpt) cc_final: 0.4123 (tpp) outliers start: 66 outliers final: 32 residues processed: 228 average time/residue: 0.5203 time to fit residues: 132.6806 Evaluate side-chains 214 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1211 PHE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1287 LYS Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1565 LYS Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 135 optimal weight: 50.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS C 39 ASN C 53 ASN C 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106997 restraints weight = 37499.088| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.33 r_work: 0.3100 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15163 Z= 0.124 Angle : 0.572 13.715 20506 Z= 0.281 Chirality : 0.041 0.404 2304 Planarity : 0.004 0.058 2420 Dihedral : 12.193 154.342 2445 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.40 % Allowed : 22.12 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.06 (0.21), residues: 1696 helix: 1.90 (0.16), residues: 984 sheet: -0.88 (0.39), residues: 144 loop : -1.02 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 994 TYR 0.016 0.001 TYR A1602 PHE 0.049 0.001 PHE A 843 TRP 0.014 0.001 TRP A 190 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15140) covalent geometry : angle 0.55294 / 0.28 (20451) SS BOND : bond 0.00353 / 0.28 ( 11) SS BOND : angle 1.31487 / 0.93 ( 22) hydrogen bonds : bond 0.04106 / 2.67 ( 831) hydrogen bonds : angle 4.22497 / 3.01 ( 2379) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00316 / 0.18 ( 3) link_BETA1-4 : angle 2.68479 / 2.06 ( 9) link_NAG-ASN : bond 0.00755 / 0.56 ( 8) link_NAG-ASN : angle 3.90076 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.5980 (t0) REVERT: A 156 GLU cc_start: 0.8059 (pp20) cc_final: 0.7812 (pp20) REVERT: A 200 TYR cc_start: 0.7170 (m-80) cc_final: 0.6819 (m-80) REVERT: A 287 GLU cc_start: 0.7539 (mp0) cc_final: 0.7096 (mp0) REVERT: A 310 LYS cc_start: 0.8808 (mttt) cc_final: 0.8525 (mtmm) REVERT: A 364 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: A 426 MET cc_start: 0.2843 (tpt) cc_final: 0.1986 (ppp) REVERT: A 733 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4770 (m-80) REVERT: A 798 MET cc_start: 0.6704 (ptt) cc_final: 0.5920 (pmt) REVERT: A 838 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7661 (ttm170) REVERT: A 890 LYS cc_start: 0.8509 (mtpp) cc_final: 0.7927 (tptt) REVERT: A 894 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 961 ASN cc_start: 0.8425 (t0) cc_final: 0.7959 (m-40) REVERT: A 994 ARG cc_start: 0.7389 (mtp85) cc_final: 0.7138 (tpt90) REVERT: A 1278 LEU cc_start: 0.7409 (tp) cc_final: 0.7117 (mm) REVERT: A 1287 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8271 (mppt) REVERT: A 1322 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: A 1378 GLN cc_start: 0.8682 (tt0) cc_final: 0.8411 (tt0) REVERT: A 1449 LEU cc_start: 0.7357 (mm) cc_final: 0.7031 (tp) REVERT: A 1462 GLN cc_start: 0.8512 (tp40) cc_final: 0.7877 (tt0) REVERT: A 1543 MET cc_start: 0.8375 (ttp) cc_final: 0.7909 (tpt) REVERT: A 1561 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 1762 ASN cc_start: 0.8310 (m-40) cc_final: 0.7959 (m-40) REVERT: A 1787 GLU cc_start: 0.1806 (OUTLIER) cc_final: 0.1439 (tp30) REVERT: A 1797 ILE cc_start: -0.0845 (OUTLIER) cc_final: -0.1182 (pt) REVERT: A 1826 MET cc_start: -0.1942 (mtm) cc_final: -0.2649 (mpp) REVERT: B 27 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 141 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8465 (mtmt) REVERT: B 170 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7545 (mp) REVERT: C 52 PHE cc_start: 0.5759 (p90) cc_final: 0.5524 (p90) REVERT: C 79 MET cc_start: 0.4418 (tpt) cc_final: 0.4135 (tpp) outliers start: 52 outliers final: 30 residues processed: 217 average time/residue: 0.5359 time to fit residues: 129.6202 Evaluate side-chains 208 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain A residue 1830 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1571 HIS C 39 ASN C 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.177282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106536 restraints weight = 34524.386| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.47 r_work: 0.3097 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15163 Z= 0.131 Angle : 0.580 13.705 20506 Z= 0.287 Chirality : 0.041 0.403 2304 Planarity : 0.004 0.061 2420 Dihedral : 12.008 152.237 2445 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.14 % Allowed : 22.38 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.11 (0.21), residues: 1696 helix: 1.93 (0.16), residues: 984 sheet: -0.79 (0.39), residues: 144 loop : -0.98 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 994 TYR 0.023 0.001 TYR A1602 PHE 0.050 0.001 PHE A 843 TRP 0.036 0.001 TRP C 67 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15140) covalent geometry : angle 0.56117 / 0.28 (20451) SS BOND : bond 0.00412 / 0.33 ( 11) SS BOND : angle 1.24398 / 0.87 ( 22) hydrogen bonds : bond 0.04194 / 2.72 ( 831) hydrogen bonds : angle 4.20399 / 3.00 ( 2379) Misc. bond : bond 0.00034 / 0.02 ( 1) link_BETA1-4 : bond 0.00323 / 0.19 ( 3) link_BETA1-4 : angle 2.71196 / 2.09 ( 9) link_NAG-ASN : bond 0.00754 / 0.55 ( 8) link_NAG-ASN : angle 3.89574 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5868 (t0) REVERT: A 156 GLU cc_start: 0.8068 (pp20) cc_final: 0.7802 (pp20) REVERT: A 200 TYR cc_start: 0.7213 (m-80) cc_final: 0.6852 (m-80) REVERT: A 287 GLU cc_start: 0.7541 (mp0) cc_final: 0.7116 (mp0) REVERT: A 310 LYS cc_start: 0.8801 (mttt) cc_final: 0.8513 (mtmm) REVERT: A 354 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9091 (mm) REVERT: A 364 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: A 426 MET cc_start: 0.2918 (tpt) cc_final: 0.2028 (ppp) REVERT: A 733 PHE cc_start: 0.5186 (OUTLIER) cc_final: 0.4885 (m-80) REVERT: A 798 MET cc_start: 0.6748 (ptt) cc_final: 0.5917 (pmt) REVERT: A 838 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7672 (ttm170) REVERT: A 890 LYS cc_start: 0.8508 (mtpp) cc_final: 0.7915 (tptt) REVERT: A 894 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7265 (mt-10) REVERT: A 961 ASN cc_start: 0.8456 (t0) cc_final: 0.7967 (m-40) REVERT: A 994 ARG cc_start: 0.7299 (mtp85) cc_final: 0.7090 (tpt90) REVERT: A 1278 LEU cc_start: 0.7466 (tp) cc_final: 0.7186 (mm) REVERT: A 1287 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8240 (mppt) REVERT: A 1322 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: A 1449 LEU cc_start: 0.7375 (mm) cc_final: 0.7042 (tp) REVERT: A 1462 GLN cc_start: 0.8516 (tp40) cc_final: 0.7873 (tt0) REVERT: A 1543 MET cc_start: 0.8380 (ttp) cc_final: 0.7926 (tpt) REVERT: A 1561 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 1762 ASN cc_start: 0.8321 (m-40) cc_final: 0.7968 (m-40) REVERT: A 1787 GLU cc_start: 0.1805 (OUTLIER) cc_final: 0.1462 (tp30) REVERT: A 1797 ILE cc_start: -0.0958 (OUTLIER) cc_final: -0.1253 (pt) REVERT: A 1826 MET cc_start: -0.1706 (mtm) cc_final: -0.2557 (mpp) REVERT: B 27 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 141 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8482 (mtmt) REVERT: B 170 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7540 (mp) REVERT: C 52 PHE cc_start: 0.5732 (p90) cc_final: 0.5505 (p90) REVERT: C 79 MET cc_start: 0.4327 (tpt) cc_final: 0.4062 (tpp) outliers start: 48 outliers final: 31 residues processed: 213 average time/residue: 0.5189 time to fit residues: 123.2762 Evaluate side-chains 213 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1211 PHE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1774 LEU Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 158 optimal weight: 0.0060 chunk 133 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 164 optimal weight: 0.0370 chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 ASN A1571 HIS C 39 ASN C 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107193 restraints weight = 35931.048| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.19 r_work: 0.3104 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15163 Z= 0.126 Angle : 0.589 13.661 20506 Z= 0.288 Chirality : 0.041 0.401 2304 Planarity : 0.004 0.061 2420 Dihedral : 11.865 150.594 2445 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.95 % Allowed : 22.38 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.15 (0.21), residues: 1696 helix: 1.93 (0.16), residues: 984 sheet: -0.75 (0.39), residues: 144 loop : -0.91 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 994 TYR 0.019 0.001 TYR A1602 PHE 0.049 0.001 PHE A 843 TRP 0.024 0.001 TRP C 67 HIS 0.003 0.001 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15140) covalent geometry : angle 0.57092 / 0.28 (20451) SS BOND : bond 0.00396 / 0.32 ( 11) SS BOND : angle 1.19578 / 0.84 ( 22) hydrogen bonds : bond 0.04137 / 2.68 ( 831) hydrogen bonds : angle 4.19456 / 2.99 ( 2379) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00330 / 0.20 ( 3) link_BETA1-4 : angle 2.69839 / 2.07 ( 9) link_NAG-ASN : bond 0.00750 / 0.55 ( 8) link_NAG-ASN : angle 3.86867 / 2.76 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5858 (t0) REVERT: A 99 ARG cc_start: 0.7512 (mtp85) cc_final: 0.7305 (mtp85) REVERT: A 156 GLU cc_start: 0.8080 (pp20) cc_final: 0.7709 (pp20) REVERT: A 157 TYR cc_start: 0.8566 (m-10) cc_final: 0.8250 (m-10) REVERT: A 200 TYR cc_start: 0.7214 (m-80) cc_final: 0.6886 (m-80) REVERT: A 287 GLU cc_start: 0.7546 (mp0) cc_final: 0.7122 (mp0) REVERT: A 310 LYS cc_start: 0.8826 (mttt) cc_final: 0.8539 (mtmm) REVERT: A 354 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9113 (mm) REVERT: A 364 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: A 426 MET cc_start: 0.3148 (tpt) cc_final: 0.2140 (ppp) REVERT: A 733 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: A 798 MET cc_start: 0.6737 (ptt) cc_final: 0.5882 (pmt) REVERT: A 838 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7684 (ttm170) REVERT: A 890 LYS cc_start: 0.8502 (mtpp) cc_final: 0.7913 (tptt) REVERT: A 894 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 961 ASN cc_start: 0.8405 (t0) cc_final: 0.7903 (m-40) REVERT: A 1278 LEU cc_start: 0.7419 (tp) cc_final: 0.7137 (mm) REVERT: A 1287 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8364 (mptt) REVERT: A 1322 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: A 1449 LEU cc_start: 0.7365 (mm) cc_final: 0.7033 (tp) REVERT: A 1462 GLN cc_start: 0.8521 (tp40) cc_final: 0.7879 (tt0) REVERT: A 1543 MET cc_start: 0.8387 (ttp) cc_final: 0.7933 (tpt) REVERT: A 1561 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: A 1762 ASN cc_start: 0.8307 (m-40) cc_final: 0.7953 (m-40) REVERT: A 1787 GLU cc_start: 0.1844 (OUTLIER) cc_final: 0.1444 (tp30) REVERT: A 1797 ILE cc_start: -0.0657 (OUTLIER) cc_final: -0.1053 (pt) REVERT: A 1826 MET cc_start: -0.2056 (mtm) cc_final: -0.2772 (mpp) REVERT: B 27 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 141 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8462 (mtmt) REVERT: B 170 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 52 PHE cc_start: 0.5820 (p90) cc_final: 0.5619 (p90) REVERT: C 79 MET cc_start: 0.4151 (tpt) cc_final: 0.3857 (tpp) outliers start: 45 outliers final: 31 residues processed: 210 average time/residue: 0.5503 time to fit residues: 128.6408 Evaluate side-chains 210 residues out of total 1528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 843 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 1211 PHE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1787 GLU Chi-restraints excluded: chain A residue 1797 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 0.0570 chunk 123 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 164 optimal weight: 0.0070 chunk 140 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 168 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 ASN A 986 ASN A1323 ASN A1571 HIS C 39 ASN C 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111080 restraints weight = 33447.470| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.04 r_work: 0.3119 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15163 Z= 0.109 Angle : 0.564 13.595 20506 Z= 0.278 Chirality : 0.041 0.391 2304 Planarity : 0.004 0.061 2420 Dihedral : 11.583 150.260 2445 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.75 % Allowed : 22.58 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.24 (0.21), residues: 1696 helix: 1.99 (0.17), residues: 990 sheet: -0.68 (0.39), residues: 144 loop : -0.88 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.020 0.001 TYR A1602 PHE 0.049 0.001 PHE A 843 TRP 0.021 0.001 TRP C 67 HIS 0.003 0.000 HIS A1837 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15140) covalent geometry : angle 0.54554 / 0.27 (20451) SS BOND : bond 0.00396 / 0.32 ( 11) SS BOND : angle 1.05125 / 0.73 ( 22) hydrogen bonds : bond 0.03781 / 2.45 ( 831) hydrogen bonds : angle 4.13077 / 2.94 ( 2379) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00376 / 0.21 ( 3) link_BETA1-4 : angle 2.61314 / 2.02 ( 9) link_NAG-ASN : bond 0.00770 / 0.57 ( 8) link_NAG-ASN : angle 3.83950 / 2.74 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6701.22 seconds wall clock time: 114 minutes 42.96 seconds (6882.96 seconds total)