Starting phenix.real_space_refine on Fri Jul 3 20:05:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w9k_32368/07_2026/7w9k_32368.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 105 5.16 5 Na 1 4.78 5 C 9862 2.51 5 N 2234 2.21 5 O 2707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 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: 14933 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1413, 11398 Classifications: {'peptide': 1413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 1362} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1413, 11398 Classifications: {'peptide': 1413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 48, 'TRANS': 1362} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 11653 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 973 Unusual residues: {' NA': 1, '1PW': 1, '9Z9': 1, 'LPE': 14, 'NAG': 2, 'PCW': 5, 'Y01': 6} Classifications: {'peptide': 3, 'undetermined': 30} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 239 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 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 190 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 190 " occ=0.50 Time building chain proxies: 4.47, per 1000 atoms: 0.30 Number of scatterers: 14933 At special positions: 0 Unit cell: (131.748, 143.825, 144.923, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 24 15.00 Na 1 11.00 O 2707 8.00 N 2234 7.00 C 9862 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=2.13 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.08 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.24 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.02 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.05 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.02 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.07 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2008 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 869.5 milliseconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 10 sheets defined 66.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.985A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 4.225A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.510A pdb=" N TYR A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 188 through 206 removed outlier: 3.611A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.995A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.030A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.829A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 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 300 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.763A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.786A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 435 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 745 through 762 Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.615A pdb=" N THR A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 833 through 847 removed outlier: 4.355A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 841 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 863 removed outlier: 3.784A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.461A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 4.127A pdb=" N ILE A 899 " --> pdb=" O CYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 removed outlier: 3.516A pdb=" N VAL A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.873A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 removed outlier: 3.627A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.552A pdb=" N ASN A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1191 through 1210 removed outlier: 3.645A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1218 Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 7.374A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1283 through 1291 removed outlier: 3.742A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1298 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 4.441A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A1304 " --> pdb=" O ALA A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1304' Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.666A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.881A 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 1445 removed outlier: 3.827A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 removed outlier: 3.531A pdb=" N ASP A1458 " --> pdb=" O GLY A1454 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A1466 " --> pdb=" O GLN A1462 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1467 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1489 Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1535 removed outlier: 3.853A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A1535 " --> pdb=" O THR A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1576 through 1600 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 3.933A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.266A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1640 removed outlier: 3.502A pdb=" N SER A1640 " --> pdb=" O ALA A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1666 Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.047A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1768 Processing helix chain 'A' and resid 1775 through 1787 removed outlier: 3.683A pdb=" N PHE A1779 " --> pdb=" O SER A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 4.482A pdb=" N SER A1803 " --> pdb=" O PHE A1799 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1826 Processing helix chain 'A' and resid 1838 through 1851 Processing helix chain 'A' and resid 1854 through 1871 removed outlier: 3.666A pdb=" N SER A1858 " --> pdb=" O GLY A1854 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.630A 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 83 through 87 removed outlier: 3.586A pdb=" N PHE B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 87' Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 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: 3.674A 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 1830 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.234A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA9, 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: 3.525A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 48 857 hydrogen bonds defined for protein. 2445 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: 2.57 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2245 1.28 - 1.42: 3899 1.42 - 1.56: 8657 1.56 - 1.71: 275 1.71 - 1.85: 172 Bond restraints: 15248 Sorted by residual: bond pdb=" C27 P5S A2019 " pdb=" C28 P5S A2019 " ideal model delta sigma weight residual 1.523 1.324 0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C ASN A1388 " pdb=" O ASN A1388 " ideal model delta sigma weight residual 1.236 1.169 0.068 7.30e-03 1.88e+04 8.58e+01 bond pdb=" C PHE A1437 " pdb=" O PHE A1437 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.19e-02 7.06e+03 7.02e+01 bond pdb=" C ILE A1442 " pdb=" O ILE A1442 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.13e-02 7.83e+03 6.96e+01 bond pdb=" CA VAL A1416 " pdb=" CB VAL A1416 " ideal model delta sigma weight residual 1.539 1.645 -0.105 1.27e-02 6.20e+03 6.88e+01 ... (remaining 15243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 17761 2.71 - 5.41: 2254 5.41 - 8.12: 458 8.12 - 10.82: 104 10.82 - 13.53: 17 Bond angle restraints: 20594 Sorted by residual: angle pdb=" N GLY A 955 " pdb=" CA GLY A 955 " pdb=" C GLY A 955 " ideal model delta sigma weight residual 112.64 125.08 -12.44 1.21e+00 6.83e-01 1.06e+02 angle pdb=" N THR A1353 " pdb=" CA THR A1353 " pdb=" C THR A1353 " ideal model delta sigma weight residual 111.28 122.31 -11.03 1.09e+00 8.42e-01 1.02e+02 angle pdb=" N LEU A 388 " pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 111.03 122.10 -11.07 1.11e+00 8.12e-01 9.94e+01 angle pdb=" N LYS B 99 " pdb=" CA LYS B 99 " pdb=" C LYS B 99 " ideal model delta sigma weight residual 113.38 102.49 10.89 1.23e+00 6.61e-01 7.83e+01 angle pdb=" N SER B 47 " pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 111.28 120.84 -9.56 1.09e+00 8.42e-01 7.69e+01 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 8681 32.09 - 64.18: 359 64.18 - 96.27: 35 96.27 - 128.36: 9 128.36 - 160.45: 4 Dihedral angle restraints: 9088 sinusoidal: 4061 harmonic: 5027 Sorted by residual: dihedral pdb=" CA PRO A1712 " pdb=" C PRO A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta harmonic sigma weight residual 180.00 45.32 134.68 0 5.00e+00 4.00e-02 7.26e+02 dihedral pdb=" C ILE A1587 " pdb=" N ILE A1587 " pdb=" CA ILE A1587 " pdb=" CB ILE A1587 " ideal model delta harmonic sigma weight residual -122.00 -135.91 13.91 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" C MET A 910 " pdb=" N MET A 910 " pdb=" CA MET A 910 " pdb=" CB MET A 910 " ideal model delta harmonic sigma weight residual -122.60 -136.14 13.54 0 2.50e+00 1.60e-01 2.93e+01 ... (remaining 9085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 2091 0.207 - 0.414: 209 0.414 - 0.621: 17 0.621 - 0.827: 0 0.827 - 1.034: 1 Chirality restraints: 2318 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 -1.83 -0.57 2.00e-02 2.50e+03 8.21e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.22e+02 chirality pdb=" C1 NAG A2008 " pdb=" ND2 ASN A1375 " pdb=" C2 NAG A2008 " pdb=" O5 NAG A2008 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 2315 not shown) Planarity restraints: 2431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.346 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG D 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2008 " 0.250 2.00e-02 2.50e+03 2.08e-01 5.41e+02 pdb=" C7 NAG A2008 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A2008 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A2008 " -0.346 2.00e-02 2.50e+03 pdb=" O7 NAG A2008 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAH 1PW A2013 " 0.108 2.00e-02 2.50e+03 1.01e-01 1.03e+02 pdb=" CAI 1PW A2013 " 0.095 2.00e-02 2.50e+03 pdb=" CAK 1PW A2013 " -0.103 2.00e-02 2.50e+03 pdb=" CAZ 1PW A2013 " -0.100 2.00e-02 2.50e+03 ... (remaining 2428 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3854 2.81 - 3.34: 14109 3.34 - 3.86: 24850 3.86 - 4.38: 30037 4.38 - 4.90: 47936 Nonbonded interactions: 120786 Sorted by model distance: nonbonded pdb=" NH2 ARG A 30 " pdb=" OD2 ASP A 84 " model vdw 2.293 3.120 nonbonded pdb=" OE2 GLU A 981 " pdb=" OAF Y01 A2005 " model vdw 2.299 3.040 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH1 ARG A 220 " model vdw 2.366 3.120 nonbonded pdb=" N PHE A1603 " pdb=" O PHE A1603 " model vdw 2.415 2.496 nonbonded pdb=" N HIS A 125 " pdb=" O HIS A 125 " model vdw 2.422 2.496 ... (remaining 120781 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: 4.240 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.019 0.205 15270 Z= 1.331 Angle : 2.108 61.880 20649 Z= 1.262 Chirality : 0.126 1.034 2318 Planarity : 0.013 0.296 2423 Dihedral : 17.078 160.448 5801 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.74 % Favored : 94.67 % Rotamer: Outliers : 2.93 % Allowed : 8.46 % Favored : 88.61 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1695 helix: -0.78 (0.15), residues: 1003 sheet: -0.54 (0.44), residues: 134 loop : -1.55 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1631 TYR 0.035 0.004 TYR A 367 PHE 0.053 0.005 PHE A 15 TRP 0.059 0.006 TRP A1786 HIS 0.020 0.005 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.01886 / 1.33 (15248) covalent geometry : angle 2.00840 / 1.24 (20594) SS BOND : bond 0.07171 / 3.84 ( 11) SS BOND : angle 8.62501 / 3.57 ( 22) hydrogen bonds : bond 0.18378 / 12.09 ( 857) hydrogen bonds : angle 7.36085 / 5.16 ( 2445) link_BETA1-4 : bond 0.02579 / 1.56 ( 3) link_BETA1-4 : angle 25.08150 / 17.45 ( 9) link_NAG-ASN : bond 0.02639 / 1.82 ( 8) link_NAG-ASN : angle 7.56196 / 5.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6184 (mtt) cc_final: 0.5653 (mtt) REVERT: A 761 MET cc_start: 0.8450 (mtm) cc_final: 0.8142 (mtm) REVERT: A 1201 MET cc_start: 0.8559 (mmp) cc_final: 0.8346 (mmp) REVERT: A 1532 MET cc_start: 0.8870 (mtt) cc_final: 0.8524 (mtt) REVERT: A 1533 MET cc_start: 0.8382 (mtt) cc_final: 0.8147 (mtp) REVERT: C 89 ASN cc_start: 0.3057 (t0) cc_final: 0.2687 (m-40) outliers start: 45 outliers final: 6 residues processed: 305 average time/residue: 0.4761 time to fit residues: 162.0725 Evaluate side-chains 178 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS A 139 ASN A 278 ASN A 336 ASN A 410 GLN A 412 ASN A 765 HIS A 766 HIS A 886 GLN A 909 HIS A 941 GLN A 961 ASN A1276 ASN A1341 ASN A1384 ASN A1461 ASN A1462 GLN A1478 GLN A1494 GLN A1709 ASN A1721 HIS A1732 ASN B 115 HIS B 143 HIS C 53 ASN C 82 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.164924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096961 restraints weight = 49297.584| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.25 r_work: 0.3153 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15270 Z= 0.166 Angle : 0.757 13.568 20649 Z= 0.377 Chirality : 0.047 0.498 2318 Planarity : 0.005 0.073 2423 Dihedral : 16.016 171.758 2503 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.05 % Rotamer: Outliers : 2.47 % Allowed : 13.80 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1695 helix: 1.13 (0.16), residues: 995 sheet: -0.50 (0.42), residues: 138 loop : -0.78 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1293 TYR 0.025 0.002 TYR A 367 PHE 0.029 0.002 PHE A 739 TRP 0.021 0.002 TRP B 173 HIS 0.016 0.002 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (15248) covalent geometry : angle 0.72921 / 0.37 (20594) SS BOND : bond 0.00310 / 0.22 ( 11) SS BOND : angle 1.55961 / 0.80 ( 22) hydrogen bonds : bond 0.05454 / 3.58 ( 857) hydrogen bonds : angle 4.76050 / 3.27 ( 2445) link_BETA1-4 : bond 0.00436 / 0.26 ( 3) link_BETA1-4 : angle 5.78981 / 4.13 ( 9) link_NAG-ASN : bond 0.00957 / 0.66 ( 8) link_NAG-ASN : angle 4.74608 / 3.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7815 (mttt) REVERT: A 98 PHE cc_start: 0.7542 (m-80) cc_final: 0.6980 (m-80) REVERT: A 1201 MET cc_start: 0.9328 (mmp) cc_final: 0.9098 (mmp) REVERT: A 1326 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8878 (mt) REVERT: A 1533 MET cc_start: 0.9018 (mtt) cc_final: 0.8779 (mtp) REVERT: A 1598 LEU cc_start: 0.8398 (tp) cc_final: 0.8175 (tt) REVERT: A 1678 MET cc_start: 0.9168 (mtp) cc_final: 0.8921 (mtp) REVERT: A 1762 ASN cc_start: 0.8288 (t0) cc_final: 0.8088 (t0) REVERT: B 65 GLU cc_start: 0.7675 (pm20) cc_final: 0.7436 (pm20) REVERT: B 66 GLU cc_start: 0.7477 (pm20) cc_final: 0.7241 (pm20) outliers start: 38 outliers final: 10 residues processed: 210 average time/residue: 0.4526 time to fit residues: 107.2940 Evaluate side-chains 172 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 129 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1363 GLN ** A1753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 118 GLN C 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.163247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095128 restraints weight = 41282.877| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.05 r_work: 0.3130 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15270 Z= 0.146 Angle : 0.644 13.140 20649 Z= 0.322 Chirality : 0.044 0.501 2318 Planarity : 0.005 0.063 2423 Dihedral : 14.681 174.361 2500 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 14.97 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1695 helix: 1.74 (0.16), residues: 999 sheet: -0.31 (0.41), residues: 141 loop : -0.63 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 115 TYR 0.025 0.002 TYR A 367 PHE 0.036 0.002 PHE A 811 TRP 0.015 0.002 TRP A1332 HIS 0.014 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (15248) covalent geometry : angle 0.61624 / 0.32 (20594) SS BOND : bond 0.00415 / 0.25 ( 11) SS BOND : angle 1.14847 / 0.72 ( 22) hydrogen bonds : bond 0.04935 / 3.22 ( 857) hydrogen bonds : angle 4.48245 / 3.08 ( 2445) link_BETA1-4 : bond 0.00766 / 0.47 ( 3) link_BETA1-4 : angle 4.78766 / 3.33 ( 9) link_NAG-ASN : bond 0.01173 / 0.78 ( 8) link_NAG-ASN : angle 4.62956 / 3.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5135 (mtp) cc_final: 0.4436 (mtt) REVERT: A 98 PHE cc_start: 0.7874 (m-80) cc_final: 0.7404 (m-80) REVERT: A 183 PHE cc_start: 0.8048 (t80) cc_final: 0.7801 (t80) REVERT: A 764 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: A 814 LEU cc_start: 0.8447 (tp) cc_final: 0.8215 (mt) REVERT: A 1532 MET cc_start: 0.9225 (mtt) cc_final: 0.8928 (mtm) REVERT: A 1533 MET cc_start: 0.9211 (mtt) cc_final: 0.8865 (mtp) REVERT: A 1570 ARG cc_start: 0.6957 (mpt-90) cc_final: 0.6302 (mpp80) REVERT: B 65 GLU cc_start: 0.7892 (pm20) cc_final: 0.7643 (pm20) REVERT: B 93 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8915 (m-40) REVERT: C 79 MET cc_start: 0.4600 (tpt) cc_final: 0.4276 (tpp) REVERT: C 113 MET cc_start: 0.4033 (OUTLIER) cc_final: 0.3812 (mmm) REVERT: C 147 LEU cc_start: 0.2286 (OUTLIER) cc_final: 0.1983 (mp) outliers start: 31 outliers final: 11 residues processed: 192 average time/residue: 0.4943 time to fit residues: 106.8324 Evaluate side-chains 169 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 0.1980 chunk 123 optimal weight: 0.0770 chunk 120 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 165 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 112 optimal weight: 0.7980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN A1363 GLN A1753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.164386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096392 restraints weight = 49857.214| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.22 r_work: 0.3142 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15270 Z= 0.113 Angle : 0.569 10.850 20649 Z= 0.283 Chirality : 0.041 0.490 2318 Planarity : 0.004 0.059 2423 Dihedral : 13.801 173.147 2500 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.69 % Allowed : 15.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.20), residues: 1695 helix: 2.03 (0.16), residues: 999 sheet: -0.20 (0.40), residues: 141 loop : -0.52 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1293 TYR 0.018 0.001 TYR A 367 PHE 0.031 0.001 PHE A 811 TRP 0.013 0.001 TRP A 849 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15248) covalent geometry : angle 0.54485 / 0.28 (20594) SS BOND : bond 0.00263 / 0.19 ( 11) SS BOND : angle 0.89597 / 0.63 ( 22) hydrogen bonds : bond 0.04249 / 2.79 ( 857) hydrogen bonds : angle 4.27620 / 2.93 ( 2445) link_BETA1-4 : bond 0.00535 / 0.33 ( 3) link_BETA1-4 : angle 4.29512 / 3.00 ( 9) link_NAG-ASN : bond 0.00869 / 0.59 ( 8) link_NAG-ASN : angle 4.02387 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7523 (m-80) cc_final: 0.7077 (m-80) REVERT: A 183 PHE cc_start: 0.7932 (t80) cc_final: 0.7658 (t80) REVERT: A 218 VAL cc_start: 0.9165 (t) cc_final: 0.8865 (t) REVERT: A 412 ASN cc_start: 0.6790 (m110) cc_final: 0.6539 (m110) REVERT: A 1533 MET cc_start: 0.9095 (mtt) cc_final: 0.8707 (mtp) REVERT: A 1570 ARG cc_start: 0.6663 (mpt-90) cc_final: 0.5745 (mpp80) REVERT: C 79 MET cc_start: 0.4597 (tpt) cc_final: 0.4204 (tpp) REVERT: C 147 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.2080 (mp) outliers start: 26 outliers final: 8 residues processed: 183 average time/residue: 0.4989 time to fit residues: 102.1261 Evaluate side-chains 162 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094505 restraints weight = 51128.863| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.96 r_work: 0.3113 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15270 Z= 0.137 Angle : 0.594 10.618 20649 Z= 0.296 Chirality : 0.042 0.492 2318 Planarity : 0.004 0.069 2423 Dihedral : 13.425 174.239 2496 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.82 % Allowed : 16.08 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.20), residues: 1695 helix: 2.19 (0.16), residues: 985 sheet: -0.03 (0.41), residues: 142 loop : -0.39 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 47 TYR 0.028 0.002 TYR A 81 PHE 0.032 0.002 PHE A 811 TRP 0.011 0.001 TRP A1549 HIS 0.011 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (15248) covalent geometry : angle 0.57036 / 0.29 (20594) SS BOND : bond 0.00281 / 0.20 ( 11) SS BOND : angle 0.87780 / 0.60 ( 22) hydrogen bonds : bond 0.04525 / 2.96 ( 857) hydrogen bonds : angle 4.25360 / 2.91 ( 2445) link_BETA1-4 : bond 0.00623 / 0.39 ( 3) link_BETA1-4 : angle 4.11568 / 2.89 ( 9) link_NAG-ASN : bond 0.00916 / 0.64 ( 8) link_NAG-ASN : angle 4.14278 / 2.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7631 (m-80) cc_final: 0.7240 (m-80) REVERT: A 183 PHE cc_start: 0.7911 (t80) cc_final: 0.7583 (t80) REVERT: A 218 VAL cc_start: 0.9061 (t) cc_final: 0.8726 (t) REVERT: A 412 ASN cc_start: 0.6809 (m110) cc_final: 0.6571 (m110) REVERT: A 791 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6779 (ttm) REVERT: A 857 LYS cc_start: 0.8254 (mttt) cc_final: 0.8031 (mtpp) REVERT: A 1533 MET cc_start: 0.9140 (mtt) cc_final: 0.8791 (mtp) REVERT: A 1570 ARG cc_start: 0.6852 (mpt-90) cc_final: 0.6021 (mpp80) REVERT: A 1597 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: A 1639 MET cc_start: 0.8889 (mmp) cc_final: 0.8597 (mmm) REVERT: A 1761 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 93 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8779 (m-40) REVERT: C 79 MET cc_start: 0.4620 (tpt) cc_final: 0.4200 (tpp) REVERT: C 113 MET cc_start: 0.4320 (tpp) cc_final: 0.3828 (tmt) REVERT: C 147 LEU cc_start: 0.2316 (OUTLIER) cc_final: 0.1988 (mp) outliers start: 28 outliers final: 12 residues processed: 174 average time/residue: 0.5212 time to fit residues: 101.5658 Evaluate side-chains 168 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1322 MET Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 167 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.160590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091038 restraints weight = 50383.055| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.24 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15270 Z= 0.174 Angle : 0.629 10.969 20649 Z= 0.316 Chirality : 0.044 0.474 2318 Planarity : 0.004 0.072 2423 Dihedral : 13.477 178.333 2496 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.50 % Allowed : 15.95 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1695 helix: 2.14 (0.16), residues: 989 sheet: 0.10 (0.41), residues: 142 loop : -0.39 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1358 TYR 0.027 0.002 TYR A 367 PHE 0.031 0.002 PHE A 811 TRP 0.012 0.002 TRP B 173 HIS 0.012 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (15248) covalent geometry : angle 0.60602 / 0.31 (20594) SS BOND : bond 0.00280 / 0.19 ( 11) SS BOND : angle 0.99423 / 0.64 ( 22) hydrogen bonds : bond 0.05037 / 3.29 ( 857) hydrogen bonds : angle 4.33960 / 2.97 ( 2445) link_BETA1-4 : bond 0.00688 / 0.43 ( 3) link_BETA1-4 : angle 4.02262 / 2.78 ( 9) link_NAG-ASN : bond 0.00804 / 0.56 ( 8) link_NAG-ASN : angle 4.25554 / 2.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7947 (m-80) cc_final: 0.7504 (m-80) REVERT: A 183 PHE cc_start: 0.8071 (t80) cc_final: 0.7854 (t80) REVERT: A 218 VAL cc_start: 0.9014 (t) cc_final: 0.8618 (t) REVERT: A 412 ASN cc_start: 0.6919 (m110) cc_final: 0.6679 (m110) REVERT: A 791 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7450 (ttm) REVERT: A 857 LYS cc_start: 0.8418 (mttt) cc_final: 0.8173 (mtpp) REVERT: A 1533 MET cc_start: 0.9258 (mtt) cc_final: 0.8855 (mtp) REVERT: A 1570 ARG cc_start: 0.7014 (mpt-90) cc_final: 0.6015 (mpp80) REVERT: A 1761 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 93 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8825 (m-40) REVERT: B 99 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (mtpt) REVERT: B 170 LEU cc_start: 0.8732 (mt) cc_final: 0.8464 (mt) REVERT: C 113 MET cc_start: 0.4399 (tpp) cc_final: 0.3976 (tmt) REVERT: C 147 LEU cc_start: 0.2309 (OUTLIER) cc_final: 0.2040 (mt) outliers start: 23 outliers final: 10 residues processed: 172 average time/residue: 0.5386 time to fit residues: 103.4629 Evaluate side-chains 164 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1193 TRP Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.161903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093198 restraints weight = 46766.839| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.25 r_work: 0.3096 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15270 Z= 0.122 Angle : 0.565 10.611 20649 Z= 0.285 Chirality : 0.041 0.474 2318 Planarity : 0.004 0.069 2423 Dihedral : 12.989 177.026 2496 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.43 % Allowed : 16.60 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.20), residues: 1695 helix: 2.28 (0.16), residues: 987 sheet: 0.26 (0.41), residues: 142 loop : -0.38 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1381 TYR 0.029 0.002 TYR A 81 PHE 0.032 0.001 PHE A 811 TRP 0.012 0.001 TRP A1549 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15248) covalent geometry : angle 0.54340 / 0.28 (20594) SS BOND : bond 0.00218 / 0.15 ( 11) SS BOND : angle 0.79174 / 0.55 ( 22) hydrogen bonds : bond 0.04358 / 2.85 ( 857) hydrogen bonds : angle 4.16156 / 2.85 ( 2445) link_BETA1-4 : bond 0.00602 / 0.37 ( 3) link_BETA1-4 : angle 3.55200 / 2.48 ( 9) link_NAG-ASN : bond 0.00891 / 0.63 ( 8) link_NAG-ASN : angle 4.00259 / 2.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7729 (m-80) cc_final: 0.7339 (m-80) REVERT: A 218 VAL cc_start: 0.8978 (t) cc_final: 0.8555 (t) REVERT: A 412 ASN cc_start: 0.6806 (m110) cc_final: 0.6586 (m110) REVERT: A 791 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7360 (ttm) REVERT: A 857 LYS cc_start: 0.8366 (mttt) cc_final: 0.8105 (mtpp) REVERT: A 1483 ASN cc_start: 0.8846 (m-40) cc_final: 0.8632 (m-40) REVERT: A 1533 MET cc_start: 0.9203 (mtt) cc_final: 0.8786 (mtp) REVERT: A 1570 ARG cc_start: 0.6945 (mpt-90) cc_final: 0.6104 (mpp80) REVERT: A 1639 MET cc_start: 0.8957 (mmp) cc_final: 0.8610 (mmm) REVERT: A 1761 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 87 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: B 93 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8839 (m-40) REVERT: B 99 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8632 (mtpt) REVERT: B 170 LEU cc_start: 0.8719 (mt) cc_final: 0.8424 (mt) REVERT: C 79 MET cc_start: 0.4935 (tpt) cc_final: 0.4726 (tpp) REVERT: C 113 MET cc_start: 0.4448 (tpp) cc_final: 0.4083 (tmt) REVERT: C 147 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.2152 (mt) outliers start: 22 outliers final: 8 residues processed: 167 average time/residue: 0.5529 time to fit residues: 102.9713 Evaluate side-chains 159 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 9 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092350 restraints weight = 52356.015| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.35 r_work: 0.3063 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15270 Z= 0.124 Angle : 0.560 10.721 20649 Z= 0.283 Chirality : 0.041 0.474 2318 Planarity : 0.004 0.074 2423 Dihedral : 12.707 179.875 2496 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.30 % Allowed : 16.60 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1695 helix: 2.36 (0.16), residues: 989 sheet: 0.39 (0.41), residues: 142 loop : -0.37 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1358 TYR 0.027 0.002 TYR A 81 PHE 0.031 0.002 PHE A 811 TRP 0.011 0.001 TRP A1549 HIS 0.009 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (15248) covalent geometry : angle 0.53877 / 0.28 (20594) SS BOND : bond 0.00415 / 0.23 ( 11) SS BOND : angle 0.78382 / 0.59 ( 22) hydrogen bonds : bond 0.04286 / 2.80 ( 857) hydrogen bonds : angle 4.10442 / 2.81 ( 2445) link_BETA1-4 : bond 0.00661 / 0.41 ( 3) link_BETA1-4 : angle 3.52533 / 2.46 ( 9) link_NAG-ASN : bond 0.00854 / 0.60 ( 8) link_NAG-ASN : angle 3.95652 / 2.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7516 (m-80) cc_final: 0.7114 (m-80) REVERT: A 218 VAL cc_start: 0.8996 (t) cc_final: 0.8587 (t) REVERT: A 791 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7133 (ttm) REVERT: A 857 LYS cc_start: 0.8322 (mttt) cc_final: 0.8078 (mtpp) REVERT: A 1483 ASN cc_start: 0.8796 (m-40) cc_final: 0.8579 (m-40) REVERT: A 1532 MET cc_start: 0.9045 (mtm) cc_final: 0.8789 (mtm) REVERT: A 1533 MET cc_start: 0.9140 (mtt) cc_final: 0.8735 (mtp) REVERT: A 1570 ARG cc_start: 0.6703 (mpt-90) cc_final: 0.5940 (mpp80) REVERT: A 1597 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: A 1761 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 93 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8754 (m-40) REVERT: B 99 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8533 (mtpt) REVERT: B 170 LEU cc_start: 0.8662 (mt) cc_final: 0.8366 (mt) REVERT: C 113 MET cc_start: 0.4622 (tpp) cc_final: 0.4289 (tmt) REVERT: C 147 LEU cc_start: 0.2429 (OUTLIER) cc_final: 0.2194 (mt) outliers start: 20 outliers final: 8 residues processed: 167 average time/residue: 0.5469 time to fit residues: 102.1956 Evaluate side-chains 166 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.161438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092698 restraints weight = 35518.395| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.90 r_work: 0.3078 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15270 Z= 0.141 Angle : 0.574 10.701 20649 Z= 0.291 Chirality : 0.042 0.472 2318 Planarity : 0.004 0.072 2423 Dihedral : 12.700 179.651 2496 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 16.80 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.20), residues: 1695 helix: 2.37 (0.16), residues: 986 sheet: 0.45 (0.41), residues: 142 loop : -0.40 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 217 TYR 0.024 0.002 TYR A 81 PHE 0.032 0.002 PHE A 811 TRP 0.011 0.001 TRP A1549 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15248) covalent geometry : angle 0.55285 / 0.29 (20594) SS BOND : bond 0.00274 / 0.17 ( 11) SS BOND : angle 0.86829 / 0.52 ( 22) hydrogen bonds : bond 0.04453 / 2.90 ( 857) hydrogen bonds : angle 4.13171 / 2.83 ( 2445) link_BETA1-4 : bond 0.00765 / 0.48 ( 3) link_BETA1-4 : angle 3.56201 / 2.48 ( 9) link_NAG-ASN : bond 0.00854 / 0.60 ( 8) link_NAG-ASN : angle 4.01943 / 2.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7892 (m-80) cc_final: 0.7551 (m-80) REVERT: A 218 VAL cc_start: 0.8988 (t) cc_final: 0.8588 (t) REVERT: A 791 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7273 (ttm) REVERT: A 857 LYS cc_start: 0.8382 (mttt) cc_final: 0.8112 (mtpp) REVERT: A 1483 ASN cc_start: 0.8884 (m-40) cc_final: 0.8666 (m-40) REVERT: A 1532 MET cc_start: 0.9057 (mtm) cc_final: 0.8826 (mtm) REVERT: A 1533 MET cc_start: 0.9205 (mtt) cc_final: 0.8816 (mtp) REVERT: A 1570 ARG cc_start: 0.6969 (mpt-90) cc_final: 0.6133 (mpp80) REVERT: A 1597 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: A 1761 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 84 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 87 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: B 93 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8823 (m-40) REVERT: B 99 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: B 170 LEU cc_start: 0.8718 (mt) cc_final: 0.8418 (mt) REVERT: C 113 MET cc_start: 0.4589 (tpp) cc_final: 0.4267 (tmt) REVERT: C 147 LEU cc_start: 0.2148 (OUTLIER) cc_final: 0.1890 (mt) outliers start: 18 outliers final: 8 residues processed: 168 average time/residue: 0.5348 time to fit residues: 99.7365 Evaluate side-chains 169 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 92 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.161630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.091981 restraints weight = 53918.735| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.14 r_work: 0.3058 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15270 Z= 0.136 Angle : 0.577 10.762 20649 Z= 0.293 Chirality : 0.041 0.472 2318 Planarity : 0.004 0.075 2423 Dihedral : 12.575 179.721 2496 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.11 % Allowed : 16.86 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1695 helix: 2.38 (0.16), residues: 989 sheet: 0.49 (0.42), residues: 142 loop : -0.38 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1358 TYR 0.021 0.002 TYR A 367 PHE 0.031 0.002 PHE A 811 TRP 0.011 0.001 TRP A1549 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15248) covalent geometry : angle 0.55635 / 0.29 (20594) SS BOND : bond 0.00264 / 0.17 ( 11) SS BOND : angle 0.86021 / 0.58 ( 22) hydrogen bonds : bond 0.04373 / 2.85 ( 857) hydrogen bonds : angle 4.10053 / 2.81 ( 2445) link_BETA1-4 : bond 0.00663 / 0.41 ( 3) link_BETA1-4 : angle 3.45764 / 2.41 ( 9) link_NAG-ASN : bond 0.00851 / 0.60 ( 8) link_NAG-ASN : angle 3.99119 / 2.71 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 PHE cc_start: 0.7659 (m-80) cc_final: 0.7283 (m-80) REVERT: A 218 VAL cc_start: 0.8932 (t) cc_final: 0.8540 (t) REVERT: A 791 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7210 (ttm) REVERT: A 798 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5706 (ptp) REVERT: A 857 LYS cc_start: 0.8291 (mttt) cc_final: 0.8028 (mtpp) REVERT: A 1483 ASN cc_start: 0.8822 (m-40) cc_final: 0.8598 (m-40) REVERT: A 1532 MET cc_start: 0.9030 (mtm) cc_final: 0.8769 (mtm) REVERT: A 1533 MET cc_start: 0.9133 (mtt) cc_final: 0.8714 (mtp) REVERT: A 1570 ARG cc_start: 0.6760 (mpt-90) cc_final: 0.5953 (mpp80) REVERT: A 1597 ASP cc_start: 0.8109 (t70) cc_final: 0.7412 (m-30) REVERT: B 84 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 87 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: B 93 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8747 (m-40) REVERT: B 99 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8518 (mtpt) REVERT: B 170 LEU cc_start: 0.8678 (mt) cc_final: 0.8369 (mt) REVERT: C 113 MET cc_start: 0.4719 (tpp) cc_final: 0.4326 (tmt) REVERT: C 147 LEU cc_start: 0.2147 (OUTLIER) cc_final: 0.1880 (mt) outliers start: 17 outliers final: 10 residues processed: 163 average time/residue: 0.5675 time to fit residues: 102.5259 Evaluate side-chains 169 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 1193 TRP Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1547 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 11 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.161456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091800 restraints weight = 50578.292| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.35 r_work: 0.3056 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15270 Z= 0.137 Angle : 0.576 10.694 20649 Z= 0.292 Chirality : 0.041 0.469 2318 Planarity : 0.004 0.072 2423 Dihedral : 12.488 178.835 2496 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.11 % Allowed : 16.80 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.20), residues: 1695 helix: 2.42 (0.16), residues: 986 sheet: 0.46 (0.41), residues: 142 loop : -0.37 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1358 TYR 0.049 0.002 TYR A1602 PHE 0.032 0.002 PHE A 811 TRP 0.011 0.001 TRP A1549 HIS 0.010 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15248) covalent geometry : angle 0.55480 / 0.29 (20594) SS BOND : bond 0.00273 / 0.18 ( 11) SS BOND : angle 0.84635 / 0.56 ( 22) hydrogen bonds : bond 0.04378 / 2.84 ( 857) hydrogen bonds : angle 4.08773 / 2.80 ( 2445) link_BETA1-4 : bond 0.00709 / 0.44 ( 3) link_BETA1-4 : angle 3.46127 / 2.42 ( 9) link_NAG-ASN : bond 0.00857 / 0.60 ( 8) link_NAG-ASN : angle 4.00048 / 2.72 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10406.23 seconds wall clock time: 176 minutes 37.38 seconds (10597.38 seconds total)