Starting phenix.real_space_refine on Fri Jul 3 15:39:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.map" model { file = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w9m_32370/07_2026/7w9m_32370.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 105 5.16 5 C 9342 2.51 5 N 2219 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 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: 14219 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11434 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1367} Chain breaks: 4 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: "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: "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: "A" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 274 Unusual residues: {'9SR': 1, 'NAG': 3, 'Y01': 5} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'LPE': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.53, per 1000 atoms: 0.25 Number of scatterers: 14219 At special positions: 0 Unit cell: (134.193, 139.648, 142.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 2 15.00 O 2551 8.00 N 2219 7.00 C 9342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.04 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.04 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-ASN " NAG A2002 " - " ASN A 283 " " NAG A2003 " - " ASN A1366 " " NAG A2009 " - " 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 B 135 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 734.2 milliseconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3258 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 65.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.706A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.529A pdb=" N VAL A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.506A pdb=" N MET A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.858A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.918A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.598A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.515A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.525A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.877A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.709A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 435 Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 745 through 763 Processing helix chain 'A' and resid 769 through 804 removed outlier: 3.504A pdb=" N THR A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Proline residue: A 800 - end of helix Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.551A pdb=" N ILE A 810 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.572A pdb=" N ASN A 853 " --> pdb=" O TRP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 3.661A pdb=" N THR A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 939 Processing helix chain 'A' and resid 940 through 977 Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1191 through 1208 removed outlier: 3.531A pdb=" N GLU A1195 " --> pdb=" O HIS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1212 Processing helix chain 'A' and resid 1219 through 1254 removed outlier: 4.209A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1291 removed outlier: 3.842A pdb=" N SER A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.657A 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 1417 removed outlier: 3.651A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1445 Processing helix chain 'A' and resid 1446 through 1467 removed outlier: 3.596A pdb=" N GLN A1462 " --> pdb=" O ASP A1458 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A1467 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 4.546A pdb=" N ILE A1508 " --> pdb=" O ILE A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.679A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1534 " --> pdb=" O VAL A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1569 Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1615 through 1626 removed outlier: 3.522A pdb=" N ARG A1619 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A1622 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A1624 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1666 removed outlier: 3.650A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1667 through 1669 No H-bonds generated for 'chain 'A' and resid 1667 through 1669' Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.228A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 removed outlier: 3.509A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Proline residue: A1706 - end of helix removed outlier: 4.187A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1751 Processing helix chain 'A' and resid 1752 through 1767 removed outlier: 4.230A pdb=" N SER A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1790 removed outlier: 3.986A pdb=" N PHE A1782 " --> pdb=" O ASP A1778 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A1788 " --> pdb=" O GLU A1784 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A1789 " --> pdb=" O VAL A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1806 removed outlier: 3.999A pdb=" N SER A1803 " --> pdb=" O PHE A1799 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP A1804 " --> pdb=" O SER A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1825 removed outlier: 3.778A pdb=" N ALA A1825 " --> pdb=" O VAL A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1851 Processing helix chain 'A' and resid 1853 through 1869 removed outlier: 3.965A pdb=" N ASP A1857 " --> pdb=" O SER A1853 " (cutoff:3.500A) Processing helix chain 'A' and resid 1873 through 1877 removed outlier: 3.808A 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: 3.624A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.817A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.573A pdb=" N ALA B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'A' and resid 1796 through 1798 Processing sheet with id=AA5, first strand: chain 'A' and resid 1829 through 1831 removed outlier: 6.590A pdb=" N MET A1830 " --> pdb=" O ILE A1880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.450A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.964A 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: 7.278A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.460A 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 48 845 hydrogen bonds defined for protein. 2391 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: 2.74 Time building geometry restraints manager: 1.79 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: 2221 1.28 - 1.43: 3832 1.43 - 1.57: 8317 1.57 - 1.71: 17 1.71 - 1.85: 172 Bond restraints: 14559 Sorted by residual: bond pdb=" C13 9SR A2001 " pdb=" N14 9SR A2001 " ideal model delta sigma weight residual 1.281 1.500 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C ARG A 838 " pdb=" O ARG A 838 " ideal model delta sigma weight residual 1.235 1.144 0.091 1.26e-02 6.30e+03 5.20e+01 bond pdb=" CA ASN B 75 " pdb=" C ASN B 75 " ideal model delta sigma weight residual 1.528 1.472 0.055 8.80e-03 1.29e+04 3.93e+01 bond pdb=" CA TRP A 363 " pdb=" C TRP A 363 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.37e-02 5.33e+03 3.26e+01 bond pdb=" CAY Y01 A2007 " pdb=" OAW Y01 A2007 " ideal model delta sigma weight residual 1.332 1.441 -0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 14554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 18965 2.64 - 5.29: 633 5.29 - 7.93: 115 7.93 - 10.57: 25 10.57 - 13.21: 7 Bond angle restraints: 19745 Sorted by residual: angle pdb=" C ARG A 838 " pdb=" N LEU A 839 " pdb=" CA LEU A 839 " ideal model delta sigma weight residual 120.28 133.49 -13.21 1.44e+00 4.82e-01 8.42e+01 angle pdb=" N LEU A 831 " pdb=" CA LEU A 831 " pdb=" C LEU A 831 " ideal model delta sigma weight residual 113.30 101.02 12.28 1.34e+00 5.57e-01 8.39e+01 angle pdb=" N MET A1678 " pdb=" CA MET A1678 " pdb=" C MET A1678 " ideal model delta sigma weight residual 110.17 98.15 12.02 1.51e+00 4.39e-01 6.33e+01 angle pdb=" N ILE A1567 " pdb=" CA ILE A1567 " pdb=" C ILE A1567 " ideal model delta sigma weight residual 113.53 105.89 7.64 9.80e-01 1.04e+00 6.08e+01 angle pdb=" N GLU A 307 " pdb=" CA GLU A 307 " pdb=" C GLU A 307 " ideal model delta sigma weight residual 111.02 120.38 -9.36 1.25e+00 6.40e-01 5.61e+01 ... (remaining 19740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.65: 8183 25.65 - 51.30: 368 51.30 - 76.95: 44 76.95 - 102.60: 13 102.60 - 128.25: 1 Dihedral angle restraints: 8609 sinusoidal: 3574 harmonic: 5035 Sorted by residual: dihedral pdb=" N ASN A 283 " pdb=" C ASN A 283 " pdb=" CA ASN A 283 " pdb=" CB ASN A 283 " ideal model delta harmonic sigma weight residual 122.80 137.32 -14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 142.23 -49.23 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" C ASN A 283 " pdb=" N ASN A 283 " pdb=" CA ASN A 283 " pdb=" CB ASN A 283 " ideal model delta harmonic sigma weight residual -122.60 -136.84 14.24 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 8606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2144 0.137 - 0.273: 114 0.273 - 0.410: 18 0.410 - 0.547: 6 0.547 - 0.684: 3 Chirality restraints: 2285 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.03e+01 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 93 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CG LEU B 174 " pdb=" CB LEU B 174 " pdb=" CD1 LEU B 174 " pdb=" CD2 LEU B 174 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.93e+00 ... (remaining 2282 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1375 " 0.261 2.00e-02 2.50e+03 3.86e-01 1.87e+03 pdb=" CG ASN A1375 " -0.121 2.00e-02 2.50e+03 pdb=" OD1 ASN A1375 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A1375 " -0.667 2.00e-02 2.50e+03 pdb=" C1 NAG A2009 " 0.463 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 93 " -0.184 2.00e-02 2.50e+03 2.10e-01 5.51e+02 pdb=" CG ASN B 93 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN B 93 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN B 93 " 0.337 2.00e-02 2.50e+03 pdb=" C1 NAG B 301 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.245 2.00e-02 2.50e+03 2.06e-01 5.28e+02 pdb=" C7 NAG E 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.003 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 113 2.57 - 3.16: 12857 3.16 - 3.74: 21651 3.74 - 4.32: 30151 4.32 - 4.90: 48940 Nonbonded interactions: 113712 Sorted by model distance: nonbonded pdb=" O VAL A1419 " pdb=" OD1 ASN A1420 " model vdw 1.992 3.040 nonbonded pdb=" O LEU A 109 " pdb=" NH1 ARG A 116 " model vdw 2.224 3.120 nonbonded pdb=" O TYR A 81 " pdb=" NZ LYS A 85 " model vdw 2.227 3.120 nonbonded pdb=" O LEU A1547 " pdb=" ND2 ASN A1551 " model vdw 2.230 3.120 nonbonded pdb=" OG SER A 318 " pdb=" OD1 ASP A 320 " model vdw 2.248 3.040 ... (remaining 113707 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.190 Find NCS groups from input model: 0.080 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.219 14579 Z= 0.711 Angle : 1.190 21.965 19795 Z= 0.672 Chirality : 0.075 0.684 2285 Planarity : 0.008 0.206 2402 Dihedral : 14.303 128.251 5321 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.90 % Favored : 93.75 % Rotamer: Outliers : 2.14 % Allowed : 9.68 % Favored : 88.17 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1699 helix: -0.21 (0.15), residues: 956 sheet: -1.99 (0.40), residues: 142 loop : -2.18 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1570 TYR 0.056 0.003 TYR A 362 PHE 0.033 0.002 PHE A 760 TRP 0.048 0.003 TRP A1408 HIS 0.011 0.002 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.70 (14559) covalent geometry : angle 1.14544 / 0.66 (19745) SS BOND : bond 0.01347 / 1.02 ( 10) SS BOND : angle 2.53401 / 1.63 ( 20) hydrogen bonds : bond 0.15834 / 10.02 ( 845) hydrogen bonds : angle 6.51142 / 4.63 ( 2391) link_BETA1-4 : bond 0.01669 / 1.04 ( 2) link_BETA1-4 : angle 2.59240 / 1.84 ( 6) link_NAG-ASN : bond 0.11924 / 7.64 ( 8) link_NAG-ASN : angle 9.03263 / 5.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 15 PHE cc_start: 0.7408 (t80) cc_final: 0.6964 (t80) REVERT: A 20 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 98 PHE cc_start: 0.8477 (m-80) cc_final: 0.8200 (m-10) REVERT: A 108 MET cc_start: 0.8442 (ttm) cc_final: 0.7891 (mmm) REVERT: A 145 MET cc_start: 0.8600 (mtp) cc_final: 0.8200 (mtp) REVERT: A 183 PHE cc_start: 0.8300 (t80) cc_final: 0.7940 (t80) REVERT: A 388 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7935 (tt) REVERT: A 405 TYR cc_start: 0.7676 (t80) cc_final: 0.7271 (t80) REVERT: A 735 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7841 (pptt) REVERT: A 764 GLU cc_start: 0.7730 (tp30) cc_final: 0.7398 (tp30) REVERT: A 768 MET cc_start: 0.6867 (mtm) cc_final: 0.6614 (mtm) REVERT: A 780 ASN cc_start: 0.8115 (t0) cc_final: 0.7904 (t0) REVERT: A 844 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8333 (ttmm) REVERT: A 1287 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8348 (mttp) REVERT: A 1470 GLN cc_start: 0.7848 (tp40) cc_final: 0.7457 (tt0) REVERT: A 1481 TYR cc_start: 0.7920 (m-80) cc_final: 0.7650 (m-80) REVERT: A 1567 ILE cc_start: 0.8462 (tp) cc_final: 0.7907 (pt) REVERT: A 1761 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 52 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7329 (tm-30) REVERT: B 62 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8271 (ttmm) REVERT: B 131 ASN cc_start: 0.7988 (t0) cc_final: 0.7527 (t0) REVERT: B 180 TYR cc_start: 0.7464 (t80) cc_final: 0.7092 (t80) REVERT: B 182 TYR cc_start: 0.8715 (t80) cc_final: 0.8469 (t80) outliers start: 33 outliers final: 10 residues processed: 287 average time/residue: 0.4896 time to fit residues: 156.9562 Evaluate side-chains 187 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1686 ASN Chi-restraints excluded: chain A residue 1759 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER 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: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 147 ASN A 154 ASN A 282 ASN A 395 ASN A 766 HIS A 809 ASN A 909 HIS A 941 GLN A 956 ASN A1478 GLN A1721 HIS B 102 GLN B 115 HIS B 134 HIS C 53 ASN C 74 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.161917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098563 restraints weight = 32988.335| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.07 r_work: 0.3062 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14579 Z= 0.141 Angle : 0.682 13.659 19795 Z= 0.335 Chirality : 0.043 0.253 2285 Planarity : 0.004 0.043 2402 Dihedral : 7.641 95.915 2027 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.05 % Allowed : 16.05 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1699 helix: 1.14 (0.16), residues: 951 sheet: -1.46 (0.39), residues: 142 loop : -1.47 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 835 TYR 0.027 0.002 TYR A 738 PHE 0.021 0.001 PHE A 165 TRP 0.024 0.001 TRP A 933 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (14559) covalent geometry : angle 0.65078 / 0.33 (19745) SS BOND : bond 0.00373 / 0.28 ( 10) SS BOND : angle 1.02578 / 0.69 ( 20) hydrogen bonds : bond 0.04954 / 3.17 ( 845) hydrogen bonds : angle 4.69882 / 3.36 ( 2391) link_BETA1-4 : bond 0.00950 / 0.56 ( 2) link_BETA1-4 : angle 0.76669 / 0.45 ( 6) link_NAG-ASN : bond 0.00690 / 0.47 ( 8) link_NAG-ASN : angle 5.84265 / 3.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8430 (tp) REVERT: A 84 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6925 (p0) REVERT: A 101 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7839 (t0) REVERT: A 106 LEU cc_start: 0.8787 (mt) cc_final: 0.8561 (pt) REVERT: A 108 MET cc_start: 0.8490 (ttm) cc_final: 0.8112 (mtp) REVERT: A 115 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7373 (tp) REVERT: A 183 PHE cc_start: 0.8358 (t80) cc_final: 0.7920 (t80) REVERT: A 217 ARG cc_start: 0.8634 (mtt90) cc_final: 0.7958 (mmm-85) REVERT: A 735 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7533 (pptt) REVERT: A 764 GLU cc_start: 0.8208 (tp30) cc_final: 0.7971 (tp30) REVERT: A 773 LYS cc_start: 0.8314 (tppt) cc_final: 0.7929 (ttmp) REVERT: A 798 MET cc_start: 0.6718 (mtt) cc_final: 0.6337 (mtt) REVERT: A 802 GLU cc_start: 0.7589 (mp0) cc_final: 0.7310 (tt0) REVERT: A 815 ILE cc_start: 0.8238 (mp) cc_final: 0.7993 (pp) REVERT: A 1251 LYS cc_start: 0.8519 (tptt) cc_final: 0.7824 (ttpt) REVERT: A 1314 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 1470 GLN cc_start: 0.8005 (tp40) cc_final: 0.7531 (mt0) REVERT: A 1481 TYR cc_start: 0.8262 (m-80) cc_final: 0.7937 (m-80) REVERT: A 1567 ILE cc_start: 0.8608 (tp) cc_final: 0.7992 (pt) REVERT: A 1605 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7089 (m) REVERT: A 1761 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 52 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7533 (tm-30) REVERT: B 93 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8281 (m-40) REVERT: B 131 ASN cc_start: 0.7878 (t0) cc_final: 0.7466 (t0) REVERT: B 148 ASP cc_start: 0.8344 (t0) cc_final: 0.8077 (t0) REVERT: B 184 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7161 (tmmm) REVERT: C 141 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5864 (tptp) outliers start: 47 outliers final: 14 residues processed: 246 average time/residue: 0.4590 time to fit residues: 126.8773 Evaluate side-chains 209 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 141 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 0.0070 chunk 51 optimal weight: 0.0270 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 282 ASN A 412 ASN C 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.162716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098984 restraints weight = 35173.239| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.23 r_work: 0.3073 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14579 Z= 0.123 Angle : 0.606 12.425 19795 Z= 0.300 Chirality : 0.040 0.200 2285 Planarity : 0.003 0.041 2402 Dihedral : 6.862 78.642 2012 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.44 % Allowed : 17.54 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1699 helix: 1.55 (0.16), residues: 953 sheet: -1.10 (0.39), residues: 142 loop : -1.29 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 835 TYR 0.017 0.001 TYR A1280 PHE 0.016 0.001 PHE A 971 TRP 0.013 0.001 TRP A 933 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14559) covalent geometry : angle 0.58680 / 0.30 (19745) SS BOND : bond 0.00293 / 0.22 ( 10) SS BOND : angle 0.79147 / 0.53 ( 20) hydrogen bonds : bond 0.04285 / 2.75 ( 845) hydrogen bonds : angle 4.39653 / 3.15 ( 2391) link_BETA1-4 : bond 0.00390 / 0.23 ( 2) link_BETA1-4 : angle 0.69324 / 0.44 ( 6) link_NAG-ASN : bond 0.00583 / 0.40 ( 8) link_NAG-ASN : angle 4.38139 / 2.52 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8595 (tp) REVERT: A 84 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6858 (p0) REVERT: A 101 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (t0) REVERT: A 106 LEU cc_start: 0.8749 (mt) cc_final: 0.8513 (pt) REVERT: A 108 MET cc_start: 0.8477 (ttm) cc_final: 0.8126 (mtp) REVERT: A 115 LEU cc_start: 0.8126 (mm) cc_final: 0.7408 (tp) REVERT: A 183 PHE cc_start: 0.8268 (t80) cc_final: 0.7921 (t80) REVERT: A 184 LEU cc_start: 0.7928 (mm) cc_final: 0.7405 (mm) REVERT: A 735 LYS cc_start: 0.7785 (mmtt) cc_final: 0.7569 (pptt) REVERT: A 764 GLU cc_start: 0.8261 (tp30) cc_final: 0.8021 (tp30) REVERT: A 820 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8415 (pp) REVERT: A 977 THR cc_start: 0.2408 (OUTLIER) cc_final: 0.2089 (t) REVERT: A 1251 LYS cc_start: 0.8455 (tptt) cc_final: 0.7748 (ttpt) REVERT: A 1314 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 1328 CYS cc_start: 0.8688 (t) cc_final: 0.8446 (m) REVERT: A 1470 GLN cc_start: 0.7990 (tp40) cc_final: 0.7485 (mt0) REVERT: A 1481 TYR cc_start: 0.8296 (m-80) cc_final: 0.8019 (m-80) REVERT: A 1561 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: A 1567 ILE cc_start: 0.8610 (tp) cc_final: 0.8358 (tp) REVERT: A 1605 SER cc_start: 0.7773 (OUTLIER) cc_final: 0.7128 (m) REVERT: A 1761 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 52 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7495 (tm-30) REVERT: B 131 ASN cc_start: 0.7927 (t0) cc_final: 0.7489 (t0) REVERT: B 184 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7259 (tmmm) REVERT: C 122 GLU cc_start: 0.3944 (tm-30) cc_final: 0.2802 (tt0) outliers start: 53 outliers final: 18 residues processed: 240 average time/residue: 0.4223 time to fit residues: 114.3599 Evaluate side-chains 202 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 129 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.161202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101901 restraints weight = 41687.170| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.95 r_work: 0.2999 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14579 Z= 0.141 Angle : 0.604 11.938 19795 Z= 0.298 Chirality : 0.040 0.187 2285 Planarity : 0.003 0.039 2402 Dihedral : 6.537 67.616 2011 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.83 % Allowed : 19.17 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1699 helix: 1.70 (0.16), residues: 953 sheet: -0.85 (0.39), residues: 142 loop : -1.22 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.023 0.002 TYR B 32 PHE 0.018 0.001 PHE B 54 TRP 0.012 0.001 TRP A1408 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14559) covalent geometry : angle 0.58704 / 0.29 (19745) SS BOND : bond 0.00798 / 0.66 ( 10) SS BOND : angle 0.89196 / 0.59 ( 20) hydrogen bonds : bond 0.04182 / 2.69 ( 845) hydrogen bonds : angle 4.32021 / 3.10 ( 2391) link_BETA1-4 : bond 0.00252 / 0.15 ( 2) link_BETA1-4 : angle 0.65180 / 0.40 ( 6) link_NAG-ASN : bond 0.00570 / 0.39 ( 8) link_NAG-ASN : angle 4.04739 / 2.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6846 (p0) REVERT: A 101 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 115 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7438 (tp) REVERT: A 184 LEU cc_start: 0.8010 (mm) cc_final: 0.7538 (mm) REVERT: A 735 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7665 (pptt) REVERT: A 798 MET cc_start: 0.6602 (mtt) cc_final: 0.6309 (mtt) REVERT: A 1251 LYS cc_start: 0.8459 (tptt) cc_final: 0.7784 (ttpt) REVERT: A 1314 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 1328 CYS cc_start: 0.8771 (t) cc_final: 0.8482 (m) REVERT: A 1470 GLN cc_start: 0.7977 (tp40) cc_final: 0.7372 (mt0) REVERT: A 1481 TYR cc_start: 0.8246 (m-80) cc_final: 0.7998 (m-80) REVERT: A 1543 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7502 (ttm) REVERT: A 1561 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: A 1673 ASP cc_start: 0.8033 (p0) cc_final: 0.7624 (p0) REVERT: A 1761 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 52 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7608 (tm-30) REVERT: B 131 ASN cc_start: 0.7991 (t0) cc_final: 0.7426 (t0) REVERT: C 122 GLU cc_start: 0.4236 (tm-30) cc_final: 0.3034 (tt0) outliers start: 59 outliers final: 26 residues processed: 232 average time/residue: 0.4454 time to fit residues: 116.5582 Evaluate side-chains 207 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 40 optimal weight: 30.0000 chunk 140 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.162288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100759 restraints weight = 38120.127| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.31 r_work: 0.3053 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14579 Z= 0.118 Angle : 0.611 15.488 19795 Z= 0.298 Chirality : 0.040 0.190 2285 Planarity : 0.003 0.052 2402 Dihedral : 6.095 57.932 2009 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.12 % Allowed : 20.01 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1699 helix: 1.83 (0.16), residues: 957 sheet: -0.62 (0.41), residues: 142 loop : -1.12 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 835 TYR 0.038 0.001 TYR C 125 PHE 0.022 0.001 PHE A 165 TRP 0.026 0.001 TRP A1408 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14559) covalent geometry : angle 0.59653 / 0.30 (19745) SS BOND : bond 0.00360 / 0.24 ( 10) SS BOND : angle 0.78154 / 0.52 ( 20) hydrogen bonds : bond 0.03917 / 2.52 ( 845) hydrogen bonds : angle 4.21545 / 3.02 ( 2391) link_BETA1-4 : bond 0.00219 / 0.13 ( 2) link_BETA1-4 : angle 0.59806 / 0.34 ( 6) link_NAG-ASN : bond 0.00586 / 0.40 ( 8) link_NAG-ASN : angle 3.85171 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.2315 (mtp) cc_final: 0.1831 (mmm) REVERT: A 84 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6704 (p0) REVERT: A 101 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7920 (t0) REVERT: A 106 LEU cc_start: 0.8840 (mt) cc_final: 0.8620 (pt) REVERT: A 108 MET cc_start: 0.8274 (mtp) cc_final: 0.7785 (mtm) REVERT: A 115 LEU cc_start: 0.8155 (mm) cc_final: 0.7422 (tp) REVERT: A 183 PHE cc_start: 0.8209 (t80) cc_final: 0.7932 (t80) REVERT: A 426 MET cc_start: 0.0098 (OUTLIER) cc_final: -0.0178 (ttp) REVERT: A 811 PHE cc_start: 0.7825 (m-10) cc_final: 0.7394 (t80) REVERT: A 820 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8394 (pp) REVERT: A 1251 LYS cc_start: 0.8350 (tptt) cc_final: 0.7676 (ttpt) REVERT: A 1314 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 1328 CYS cc_start: 0.8725 (t) cc_final: 0.8469 (m) REVERT: A 1470 GLN cc_start: 0.7915 (tp40) cc_final: 0.7338 (mt0) REVERT: A 1481 TYR cc_start: 0.8251 (m-80) cc_final: 0.8010 (m-80) REVERT: A 1561 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: A 1605 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7089 (m) REVERT: A 1673 ASP cc_start: 0.7921 (p0) cc_final: 0.7519 (p0) REVERT: A 1761 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 52 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7540 (tm-30) REVERT: B 131 ASN cc_start: 0.7901 (t0) cc_final: 0.7337 (t0) REVERT: B 185 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7090 (mp) REVERT: C 62 GLN cc_start: 0.8549 (mt0) cc_final: 0.8064 (mp10) REVERT: C 122 GLU cc_start: 0.4298 (tm-30) cc_final: 0.3214 (tt0) outliers start: 48 outliers final: 19 residues processed: 232 average time/residue: 0.4017 time to fit residues: 105.9116 Evaluate side-chains 201 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 140 optimal weight: 0.0980 chunk 167 optimal weight: 40.0000 chunk 50 optimal weight: 30.0000 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 408 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.160377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096317 restraints weight = 39892.265| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.28 r_work: 0.3025 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14579 Z= 0.177 Angle : 0.638 12.722 19795 Z= 0.313 Chirality : 0.042 0.202 2285 Planarity : 0.004 0.038 2402 Dihedral : 6.102 59.285 2009 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.83 % Allowed : 20.92 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1699 helix: 1.79 (0.16), residues: 956 sheet: -0.62 (0.40), residues: 145 loop : -1.11 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.023 0.002 TYR B 32 PHE 0.021 0.001 PHE A 971 TRP 0.012 0.001 TRP A 808 HIS 0.006 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (14559) covalent geometry : angle 0.62261 / 0.31 (19745) SS BOND : bond 0.00270 / 0.18 ( 10) SS BOND : angle 1.23625 / 0.85 ( 20) hydrogen bonds : bond 0.04276 / 2.75 ( 845) hydrogen bonds : angle 4.29656 / 3.07 ( 2391) link_BETA1-4 : bond 0.00124 / 0.07 ( 2) link_BETA1-4 : angle 0.68910 / 0.48 ( 6) link_NAG-ASN : bond 0.00588 / 0.40 ( 8) link_NAG-ASN : angle 3.86097 / 2.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6674 (p0) REVERT: A 106 LEU cc_start: 0.8844 (mt) cc_final: 0.8598 (pt) REVERT: A 108 MET cc_start: 0.8275 (mtp) cc_final: 0.7772 (mtm) REVERT: A 184 LEU cc_start: 0.7966 (mm) cc_final: 0.7459 (mm) REVERT: A 364 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: A 426 MET cc_start: 0.0458 (OUTLIER) cc_final: 0.0108 (ttp) REVERT: A 798 MET cc_start: 0.6674 (mtt) cc_final: 0.6433 (mtt) REVERT: A 1251 LYS cc_start: 0.8380 (tptt) cc_final: 0.7705 (ttpt) REVERT: A 1314 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 1328 CYS cc_start: 0.8745 (t) cc_final: 0.8497 (m) REVERT: A 1470 GLN cc_start: 0.7930 (tp40) cc_final: 0.7416 (mt0) REVERT: A 1481 TYR cc_start: 0.8237 (m-80) cc_final: 0.7956 (m-80) REVERT: A 1561 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: A 1567 ILE cc_start: 0.8518 (tp) cc_final: 0.7931 (pt) REVERT: A 1673 ASP cc_start: 0.7930 (p0) cc_final: 0.7552 (p0) REVERT: A 1761 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 52 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7594 (tm-30) REVERT: B 131 ASN cc_start: 0.7883 (t0) cc_final: 0.7193 (t0) REVERT: C 62 GLN cc_start: 0.8490 (mt0) cc_final: 0.8285 (mt0) REVERT: C 79 MET cc_start: 0.5715 (tpt) cc_final: 0.5048 (tpt) REVERT: C 86 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8558 (tptp) REVERT: C 122 GLU cc_start: 0.4404 (tm-30) cc_final: 0.3189 (tt0) outliers start: 59 outliers final: 28 residues processed: 222 average time/residue: 0.4199 time to fit residues: 105.7746 Evaluate side-chains 207 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 408 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099130 restraints weight = 40360.194| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.43 r_work: 0.3019 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14579 Z= 0.139 Angle : 0.618 11.833 19795 Z= 0.301 Chirality : 0.041 0.189 2285 Planarity : 0.003 0.039 2402 Dihedral : 5.932 57.609 2009 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.79 % Allowed : 21.90 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1699 helix: 1.90 (0.16), residues: 955 sheet: -0.43 (0.42), residues: 145 loop : -1.07 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 835 TYR 0.028 0.001 TYR B 32 PHE 0.018 0.001 PHE B 54 TRP 0.015 0.001 TRP A 808 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (14559) covalent geometry : angle 0.60366 / 0.30 (19745) SS BOND : bond 0.00301 / 0.22 ( 10) SS BOND : angle 1.02005 / 0.70 ( 20) hydrogen bonds : bond 0.04041 / 2.61 ( 845) hydrogen bonds : angle 4.22224 / 3.02 ( 2391) link_BETA1-4 : bond 0.00215 / 0.13 ( 2) link_BETA1-4 : angle 0.73499 / 0.48 ( 6) link_NAG-ASN : bond 0.00585 / 0.40 ( 8) link_NAG-ASN : angle 3.74785 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.2541 (mtp) cc_final: 0.2119 (mmm) REVERT: A 84 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6637 (p0) REVERT: A 106 LEU cc_start: 0.8840 (mt) cc_final: 0.8587 (pt) REVERT: A 108 MET cc_start: 0.8300 (mtp) cc_final: 0.7785 (mtm) REVERT: A 184 LEU cc_start: 0.7930 (mm) cc_final: 0.7407 (mm) REVERT: A 217 ARG cc_start: 0.8478 (mtm110) cc_final: 0.7879 (mtm-85) REVERT: A 364 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: A 426 MET cc_start: 0.0365 (OUTLIER) cc_final: 0.0045 (ttp) REVERT: A 1251 LYS cc_start: 0.8345 (tptt) cc_final: 0.7665 (ttpt) REVERT: A 1314 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 1328 CYS cc_start: 0.8714 (t) cc_final: 0.8457 (m) REVERT: A 1329 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 1470 GLN cc_start: 0.7877 (tp40) cc_final: 0.7308 (mt0) REVERT: A 1481 TYR cc_start: 0.8226 (m-80) cc_final: 0.7962 (m-80) REVERT: A 1543 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7465 (ttm) REVERT: A 1561 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: A 1567 ILE cc_start: 0.8438 (tp) cc_final: 0.7881 (pt) REVERT: A 1673 ASP cc_start: 0.7889 (p0) cc_final: 0.7538 (p0) REVERT: A 1761 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 131 ASN cc_start: 0.7946 (t0) cc_final: 0.7246 (t0) REVERT: C 79 MET cc_start: 0.5755 (tpt) cc_final: 0.5277 (tpt) REVERT: C 86 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8602 (tptp) REVERT: C 122 GLU cc_start: 0.4203 (tm-30) cc_final: 0.3230 (tt0) REVERT: C 125 TYR cc_start: 0.5195 (m-80) cc_final: 0.4624 (m-80) outliers start: 43 outliers final: 22 residues processed: 210 average time/residue: 0.3905 time to fit residues: 93.0472 Evaluate side-chains 205 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 6 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 282 ASN A 424 GLN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.160860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096308 restraints weight = 41851.655| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.84 r_work: 0.3033 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14579 Z= 0.146 Angle : 0.616 11.080 19795 Z= 0.302 Chirality : 0.041 0.201 2285 Planarity : 0.003 0.038 2402 Dihedral : 5.833 57.782 2009 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.66 % Allowed : 22.42 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1699 helix: 1.93 (0.16), residues: 955 sheet: -0.39 (0.42), residues: 142 loop : -1.06 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.026 0.001 TYR B 32 PHE 0.032 0.001 PHE A 183 TRP 0.011 0.001 TRP A 808 HIS 0.004 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (14559) covalent geometry : angle 0.60273 / 0.30 (19745) SS BOND : bond 0.00302 / 0.23 ( 10) SS BOND : angle 0.95560 / 0.66 ( 20) hydrogen bonds : bond 0.04045 / 2.61 ( 845) hydrogen bonds : angle 4.22165 / 3.02 ( 2391) link_BETA1-4 : bond 0.00232 / 0.14 ( 2) link_BETA1-4 : angle 0.67207 / 0.47 ( 6) link_NAG-ASN : bond 0.00548 / 0.38 ( 8) link_NAG-ASN : angle 3.68170 / 1.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.2963 (mtp) cc_final: 0.2424 (mmm) REVERT: A 84 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6655 (p0) REVERT: A 108 MET cc_start: 0.8287 (mtp) cc_final: 0.7939 (mtm) REVERT: A 184 LEU cc_start: 0.7831 (mm) cc_final: 0.7381 (mm) REVERT: A 217 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7856 (mtm-85) REVERT: A 364 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: A 426 MET cc_start: 0.0498 (OUTLIER) cc_final: 0.0203 (ttp) REVERT: A 811 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7257 (t80) REVERT: A 1251 LYS cc_start: 0.8366 (tptt) cc_final: 0.7699 (ttpt) REVERT: A 1314 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (tt) REVERT: A 1328 CYS cc_start: 0.8745 (t) cc_final: 0.8499 (m) REVERT: A 1329 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 1470 GLN cc_start: 0.7940 (tp40) cc_final: 0.7407 (mt0) REVERT: A 1481 TYR cc_start: 0.8264 (m-80) cc_final: 0.7977 (m-80) REVERT: A 1543 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7423 (ttm) REVERT: A 1561 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: A 1567 ILE cc_start: 0.8467 (tp) cc_final: 0.7935 (pt) REVERT: A 1673 ASP cc_start: 0.7868 (p0) cc_final: 0.7499 (p0) REVERT: A 1761 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 131 ASN cc_start: 0.7880 (t0) cc_final: 0.7165 (t0) REVERT: C 62 GLN cc_start: 0.8603 (mt0) cc_final: 0.8161 (mp10) REVERT: C 79 MET cc_start: 0.5846 (tpt) cc_final: 0.5510 (tpt) REVERT: C 122 GLU cc_start: 0.4449 (tm-30) cc_final: 0.3526 (tt0) outliers start: 41 outliers final: 21 residues processed: 212 average time/residue: 0.3923 time to fit residues: 94.2045 Evaluate side-chains 206 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.102846 restraints weight = 44066.323| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.71 r_work: 0.3033 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14579 Z= 0.118 Angle : 0.629 14.035 19795 Z= 0.301 Chirality : 0.041 0.352 2285 Planarity : 0.003 0.039 2402 Dihedral : 5.638 57.960 2009 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.14 % Allowed : 23.52 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1699 helix: 2.01 (0.16), residues: 954 sheet: -0.25 (0.43), residues: 142 loop : -1.03 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.032 0.001 TYR B 32 PHE 0.027 0.001 PHE A 165 TRP 0.017 0.001 TRP A 808 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (14559) covalent geometry : angle 0.61667 / 0.30 (19745) SS BOND : bond 0.00245 / 0.18 ( 10) SS BOND : angle 0.78963 / 0.54 ( 20) hydrogen bonds : bond 0.03804 / 2.47 ( 845) hydrogen bonds : angle 4.18113 / 3.00 ( 2391) link_BETA1-4 : bond 0.00307 / 0.19 ( 2) link_BETA1-4 : angle 0.74289 / 0.48 ( 6) link_NAG-ASN : bond 0.00543 / 0.37 ( 8) link_NAG-ASN : angle 3.51806 / 1.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6724 (p0) REVERT: A 106 LEU cc_start: 0.8816 (mt) cc_final: 0.8567 (pt) REVERT: A 108 MET cc_start: 0.8233 (mtp) cc_final: 0.7685 (mtm) REVERT: A 217 ARG cc_start: 0.8465 (mtm110) cc_final: 0.7894 (mtm-85) REVERT: A 240 GLN cc_start: 0.8309 (tp40) cc_final: 0.8075 (mp10) REVERT: A 364 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: A 426 MET cc_start: 0.0464 (OUTLIER) cc_final: 0.0113 (ttp) REVERT: A 798 MET cc_start: 0.6496 (mtt) cc_final: 0.6077 (tpt) REVERT: A 811 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7250 (t80) REVERT: A 854 MET cc_start: 0.7746 (tpt) cc_final: 0.7033 (tpt) REVERT: A 902 ASP cc_start: 0.8673 (m-30) cc_final: 0.8385 (p0) REVERT: A 1251 LYS cc_start: 0.8370 (tptt) cc_final: 0.7722 (ttpt) REVERT: A 1314 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 1328 CYS cc_start: 0.8770 (t) cc_final: 0.8552 (m) REVERT: A 1329 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (mp) REVERT: A 1481 TYR cc_start: 0.8276 (m-80) cc_final: 0.7982 (m-80) REVERT: A 1543 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7524 (ttm) REVERT: A 1561 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: A 1673 ASP cc_start: 0.7872 (p0) cc_final: 0.7543 (p0) REVERT: A 1761 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 131 ASN cc_start: 0.7915 (t0) cc_final: 0.7178 (t0) REVERT: C 79 MET cc_start: 0.5986 (tpt) cc_final: 0.5491 (tpt) REVERT: C 122 GLU cc_start: 0.4341 (tm-30) cc_final: 0.3430 (tt0) REVERT: C 125 TYR cc_start: 0.5111 (m-80) cc_final: 0.4683 (m-80) outliers start: 33 outliers final: 21 residues processed: 205 average time/residue: 0.4341 time to fit residues: 100.8665 Evaluate side-chains 200 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 144 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 chunk 163 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101878 restraints weight = 42612.920| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.97 r_work: 0.2997 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14579 Z= 0.151 Angle : 0.649 12.694 19795 Z= 0.313 Chirality : 0.042 0.277 2285 Planarity : 0.003 0.038 2402 Dihedral : 5.671 58.520 2009 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.14 % Allowed : 23.72 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1699 helix: 1.91 (0.16), residues: 962 sheet: -0.27 (0.43), residues: 142 loop : -1.02 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.029 0.001 TYR B 32 PHE 0.025 0.001 PHE A 183 TRP 0.016 0.001 TRP A 808 HIS 0.006 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14559) covalent geometry : angle 0.63732 / 0.31 (19745) SS BOND : bond 0.00301 / 0.22 ( 10) SS BOND : angle 0.90764 / 0.62 ( 20) hydrogen bonds : bond 0.04000 / 2.59 ( 845) hydrogen bonds : angle 4.21656 / 3.02 ( 2391) link_BETA1-4 : bond 0.00149 / 0.09 ( 2) link_BETA1-4 : angle 0.73298 / 0.50 ( 6) link_NAG-ASN : bond 0.00527 / 0.36 ( 8) link_NAG-ASN : angle 3.49988 / 1.88 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6719 (p0) REVERT: A 106 LEU cc_start: 0.8815 (mt) cc_final: 0.8567 (pt) REVERT: A 108 MET cc_start: 0.8227 (mtp) cc_final: 0.7690 (mtm) REVERT: A 217 ARG cc_start: 0.8507 (mtm110) cc_final: 0.7921 (mtm-85) REVERT: A 240 GLN cc_start: 0.8288 (tp40) cc_final: 0.8044 (mp10) REVERT: A 364 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: A 426 MET cc_start: 0.0453 (OUTLIER) cc_final: 0.0094 (ttp) REVERT: A 798 MET cc_start: 0.6505 (mtt) cc_final: 0.6066 (tpt) REVERT: A 811 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7245 (t80) REVERT: A 854 MET cc_start: 0.7813 (tpt) cc_final: 0.7088 (tpt) REVERT: A 902 ASP cc_start: 0.8663 (m-30) cc_final: 0.8361 (p0) REVERT: A 1251 LYS cc_start: 0.8373 (tptt) cc_final: 0.7705 (ttpt) REVERT: A 1314 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 1328 CYS cc_start: 0.8753 (t) cc_final: 0.8503 (m) REVERT: A 1329 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 1481 TYR cc_start: 0.8305 (m-80) cc_final: 0.8030 (m-80) REVERT: A 1543 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7461 (ttm) REVERT: A 1561 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: A 1567 ILE cc_start: 0.8425 (tp) cc_final: 0.7852 (pt) REVERT: A 1673 ASP cc_start: 0.7896 (p0) cc_final: 0.7538 (p0) REVERT: A 1761 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 93 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8419 (m-40) REVERT: B 131 ASN cc_start: 0.7865 (t0) cc_final: 0.7097 (t0) REVERT: C 62 GLN cc_start: 0.8671 (mt0) cc_final: 0.7927 (mp10) REVERT: C 79 MET cc_start: 0.5998 (tpt) cc_final: 0.5497 (tpt) REVERT: C 122 GLU cc_start: 0.4380 (tm-30) cc_final: 0.3449 (tt0) REVERT: C 125 TYR cc_start: 0.4856 (m-80) cc_final: 0.4510 (m-80) outliers start: 33 outliers final: 19 residues processed: 201 average time/residue: 0.4432 time to fit residues: 100.3355 Evaluate side-chains 199 residues out of total 1534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1831 VAL Chi-restraints excluded: chain A residue 1841 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 5 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101966 restraints weight = 52403.241| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.86 r_work: 0.3029 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14579 Z= 0.119 Angle : 0.629 12.703 19795 Z= 0.302 Chirality : 0.041 0.282 2285 Planarity : 0.003 0.047 2402 Dihedral : 5.538 59.029 2009 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.08 % Allowed : 23.91 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1699 helix: 1.99 (0.16), residues: 963 sheet: -0.18 (0.43), residues: 142 loop : -0.98 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 135 TYR 0.032 0.001 TYR B 32 PHE 0.029 0.001 PHE A 98 TRP 0.016 0.001 TRP A 808 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14559) covalent geometry : angle 0.61841 / 0.30 (19745) SS BOND : bond 0.00269 / 0.20 ( 10) SS BOND : angle 0.75367 / 0.52 ( 20) hydrogen bonds : bond 0.03761 / 2.43 ( 845) hydrogen bonds : angle 4.16871 / 2.98 ( 2391) link_BETA1-4 : bond 0.00322 / 0.19 ( 2) link_BETA1-4 : angle 0.76819 / 0.49 ( 6) link_NAG-ASN : bond 0.00530 / 0.36 ( 8) link_NAG-ASN : angle 3.35757 / 1.80 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.43 seconds wall clock time: 94 minutes 7.20 seconds (5647.20 seconds total)