Starting phenix.real_space_refine on Sun Nov 17 21:11:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r76_24292/11_2024/7r76_24292.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Zn 5 6.06 5 S 70 5.16 5 C 9110 2.51 5 N 2618 2.21 5 O 2697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14500 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 14495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1834, 14495 Classifications: {'peptide': 1834} Link IDs: {'PTRANS': 87, 'TRANS': 1746} Chain breaks: 12 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3901 SG CYS A 817 65.300 71.049 59.881 1.00 27.86 S ATOM 4070 SG CYS A 840 64.138 70.427 62.594 1.00 36.46 S ATOM 6757 SG CYS A1200 35.447 41.622 32.165 1.00 49.78 S ATOM 7317 SG CYS A1271 36.470 38.322 33.356 1.00 55.95 S ATOM 7343 SG CYS A1274 38.614 41.235 34.267 1.00 44.52 S ATOM 4006 SG CYS A 832 73.245 82.398 62.158 1.00 30.72 S ATOM 4030 SG CYS A 835 74.721 81.523 59.071 1.00 29.72 S ATOM 5857 SG CYS A1065 77.556 81.600 61.527 1.00 32.95 S ATOM 12873 SG CYS A2099 83.672 70.513 103.241 1.00109.17 S Time building chain proxies: 8.70, per 1000 atoms: 0.60 Number of scatterers: 14500 At special positions: 0 Unit cell: (125.552, 110.656, 133, 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) Zn 5 29.99 S 70 16.00 O 2697 8.00 N 2618 7.00 C 9110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2401 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 817 " pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" ND1 HIS A1348 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1200 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1274 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" ND1 HIS A2101 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2099 " Number of angles added : 3 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3474 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 39.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.200A pdb=" N ASN A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.783A pdb=" N ILE A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 3.911A pdb=" N VAL A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 460 through 474 removed outlier: 3.682A pdb=" N GLY A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 534 through 544 removed outlier: 3.816A pdb=" N LYS A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.620A pdb=" N LEU A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.916A pdb=" N SER A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.632A pdb=" N LEU A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.642A pdb=" N LEU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 750 Processing helix chain 'A' and resid 759 through 780 removed outlier: 3.779A pdb=" N GLU A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 766 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.532A pdb=" N CYS A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 870 removed outlier: 3.885A pdb=" N LYS A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 867 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 896 removed outlier: 4.184A pdb=" N LYS A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 918 removed outlier: 3.876A pdb=" N ALA A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 975 Processing helix chain 'A' and resid 1019 through 1025 Processing helix chain 'A' and resid 1044 through 1050 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1187 through 1195 removed outlier: 3.822A pdb=" N ILE A1191 " --> pdb=" O SER A1187 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1243 removed outlier: 6.769A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A1238 " --> pdb=" O HIS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 Processing helix chain 'A' and resid 1306 through 1319 removed outlier: 3.667A pdb=" N GLN A1312 " --> pdb=" O LEU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1353 removed outlier: 3.673A pdb=" N ARG A1353 " --> pdb=" O ARG A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1422 removed outlier: 3.795A pdb=" N TRP A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1419 " --> pdb=" O TRP A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1480 removed outlier: 3.657A pdb=" N THR A1480 " --> pdb=" O LEU A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1508 Processing helix chain 'A' and resid 1510 through 1518 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1552 through 1557 removed outlier: 3.807A pdb=" N GLU A1556 " --> pdb=" O SER A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1557 through 1569 removed outlier: 3.843A pdb=" N TRP A1561 " --> pdb=" O SER A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1601 removed outlier: 3.617A pdb=" N ALA A1591 " --> pdb=" O ARG A1587 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A1596 " --> pdb=" O MET A1592 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER A1597 " --> pdb=" O GLU A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1717 removed outlier: 3.561A pdb=" N MET A1716 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A1717 " --> pdb=" O LEU A1714 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1713 through 1717' Processing helix chain 'A' and resid 1734 through 1741 removed outlier: 3.509A pdb=" N VAL A1738 " --> pdb=" O SER A1734 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A1740 " --> pdb=" O ALA A1736 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A1741 " --> pdb=" O ALA A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1769 removed outlier: 3.949A pdb=" N SER A1763 " --> pdb=" O ALA A1759 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A1764 " --> pdb=" O ALA A1760 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A1767 " --> pdb=" O SER A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1790 removed outlier: 3.894A pdb=" N LYS A1786 " --> pdb=" O VAL A1782 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1787 " --> pdb=" O GLN A1783 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A1788 " --> pdb=" O TYR A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1795 through 1803 removed outlier: 4.148A pdb=" N PHE A1801 " --> pdb=" O LYS A1797 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A1803 " --> pdb=" O HIS A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1825 removed outlier: 3.723A pdb=" N ARG A1813 " --> pdb=" O TRP A1809 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1823 " --> pdb=" O GLU A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1865 removed outlier: 3.719A pdb=" N LEU A1857 " --> pdb=" O VAL A1853 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A1858 " --> pdb=" O TYR A1854 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A1859 " --> pdb=" O LEU A1855 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1887 removed outlier: 3.849A pdb=" N ASP A1881 " --> pdb=" O VAL A1877 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG A1882 " --> pdb=" O SER A1878 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1883 " --> pdb=" O GLN A1879 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A1886 " --> pdb=" O ARG A1882 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1890 No H-bonds generated for 'chain 'A' and resid 1888 through 1890' Processing helix chain 'A' and resid 1895 through 1906 Processing helix chain 'A' and resid 1920 through 1961 removed outlier: 3.774A pdb=" N HIS A1927 " --> pdb=" O GLU A1923 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A1957 " --> pdb=" O LEU A1953 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A1958 " --> pdb=" O HIS A1954 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A1960 " --> pdb=" O TRP A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1977 Processing helix chain 'A' and resid 1992 through 2000 removed outlier: 3.657A pdb=" N LEU A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A1997 " --> pdb=" O ALA A1993 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2068 Processing helix chain 'A' and resid 2069 through 2077 Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 4.729A pdb=" N LYS A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2132 removed outlier: 3.615A pdb=" N ILE A2132 " --> pdb=" O PRO A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2150 through 2163 Processing helix chain 'A' and resid 2175 through 2190 removed outlier: 4.086A pdb=" N LYS A2181 " --> pdb=" O ASP A2177 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A2187 " --> pdb=" O SER A2183 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A2188 " --> pdb=" O GLU A2184 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A2189 " --> pdb=" O ALA A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2209 Processing helix chain 'A' and resid 2251 through 2268 removed outlier: 4.431A pdb=" N ALA A2262 " --> pdb=" O VAL A2258 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A2265 " --> pdb=" O GLN A2261 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A2266 " --> pdb=" O ALA A2262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A2267 " --> pdb=" O ILE A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2285 through 2299 removed outlier: 3.792A pdb=" N ALA A2293 " --> pdb=" O THR A2289 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A2297 " --> pdb=" O ALA A2293 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A2299 " --> pdb=" O ARG A2295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 8.128A pdb=" N PHE A 406 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER A 385 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 347 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 383 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 349 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER A 385 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A 351 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 434 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 508 removed outlier: 3.555A pdb=" N THR A 526 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 503 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 524 " --> pdb=" O GLN A 503 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 665 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.437A pdb=" N ILE A 783 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A1207 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 782 through 783 removed outlier: 7.437A pdb=" N ILE A 783 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A1207 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA A1205 " --> pdb=" O LEU A1341 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A1341 " --> pdb=" O ALA A1205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA7, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 7.222A pdb=" N SER A1037 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A1034 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1017 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP A1036 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU A1015 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A1144 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS A1004 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP A1142 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A1006 " --> pdb=" O LYS A1140 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS A1140 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A1008 " --> pdb=" O LYS A1138 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS A1138 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A1010 " --> pdb=" O GLN A1136 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A1136 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 7.222A pdb=" N SER A1037 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A1034 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A1017 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP A1036 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU A1015 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 980 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A 926 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU A 938 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE A 924 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1091 through 1092 removed outlier: 3.920A pdb=" N ARG A1103 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1281 through 1283 Processing sheet with id=AB2, first strand: chain 'A' and resid 1364 through 1370 Processing sheet with id=AB3, first strand: chain 'A' and resid 1458 through 1460 removed outlier: 6.679A pdb=" N GLY A1459 " --> pdb=" O ILE A1748 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG A1720 " --> pdb=" O TYR A1745 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N TRP A1747 " --> pdb=" O ARG A1720 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A1722 " --> pdb=" O TRP A1747 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A1499 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N MET A1550 " --> pdb=" O THR A1499 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1501 " --> pdb=" O MET A1550 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A1551 " --> pdb=" O ILE A1528 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1838 through 1844 removed outlier: 6.291A pdb=" N VAL A1838 " --> pdb=" O ILE A2277 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ARG A2279 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS A1840 " --> pdb=" O ARG A2279 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A2281 " --> pdb=" O HIS A1840 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS A1842 " --> pdb=" O LEU A2281 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2094 through 2095 530 hydrogen bonds defined for protein. 1527 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: 7.32 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4726 1.34 - 1.46: 2735 1.46 - 1.58: 7227 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 14788 Sorted by residual: bond pdb=" N CYS A 817 " pdb=" CA CYS A 817 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.24e-02 6.50e+03 1.12e+01 bond pdb=" N VAL A1105 " pdb=" CA VAL A1105 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.39e+00 bond pdb=" N ASP A 625 " pdb=" CA ASP A 625 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.21e+00 bond pdb=" N TYR A1104 " pdb=" CA TYR A1104 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.06e+00 bond pdb=" N ALA A2262 " pdb=" CA ALA A2262 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.04e+00 ... (remaining 14783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 19540 2.87 - 5.73: 408 5.73 - 8.60: 49 8.60 - 11.46: 12 11.46 - 14.33: 1 Bond angle restraints: 20010 Sorted by residual: angle pdb=" N ILE A2263 " pdb=" CA ILE A2263 " pdb=" C ILE A2263 " ideal model delta sigma weight residual 112.50 102.14 10.36 1.39e+00 5.18e-01 5.56e+01 angle pdb=" N GLU A 572 " pdb=" CA GLU A 572 " pdb=" CB GLU A 572 " ideal model delta sigma weight residual 110.28 119.28 -9.00 1.55e+00 4.16e-01 3.37e+01 angle pdb=" N SER A 530 " pdb=" CA SER A 530 " pdb=" C SER A 530 " ideal model delta sigma weight residual 113.41 106.69 6.72 1.22e+00 6.72e-01 3.04e+01 angle pdb=" C GLN A2261 " pdb=" N ALA A2262 " pdb=" CA ALA A2262 " ideal model delta sigma weight residual 121.54 131.88 -10.34 1.91e+00 2.74e-01 2.93e+01 angle pdb=" C LEU A1091 " pdb=" N ASP A1092 " pdb=" CA ASP A1092 " ideal model delta sigma weight residual 122.64 116.15 6.49 1.25e+00 6.40e-01 2.70e+01 ... (remaining 20005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 8014 17.74 - 35.48: 826 35.48 - 53.21: 140 53.21 - 70.95: 27 70.95 - 88.69: 18 Dihedral angle restraints: 9025 sinusoidal: 3702 harmonic: 5323 Sorted by residual: dihedral pdb=" CA SER A2013 " pdb=" C SER A2013 " pdb=" N PRO A2014 " pdb=" CA PRO A2014 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA HIS A1805 " pdb=" C HIS A1805 " pdb=" N SER A1806 " pdb=" CA SER A1806 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA HIS A 849 " pdb=" C HIS A 849 " pdb=" N VAL A 850 " pdb=" CA VAL A 850 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 9022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1911 0.080 - 0.160: 301 0.160 - 0.241: 13 0.241 - 0.321: 5 0.321 - 0.401: 3 Chirality restraints: 2233 Sorted by residual: chirality pdb=" CB ILE A 663 " pdb=" CA ILE A 663 " pdb=" CG1 ILE A 663 " pdb=" CG2 ILE A 663 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ILE A2263 " pdb=" N ILE A2263 " pdb=" C ILE A2263 " pdb=" CB ILE A2263 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR A 613 " pdb=" CA THR A 613 " pdb=" OG1 THR A 613 " pdb=" CG2 THR A 613 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2230 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A2261 " 0.025 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C GLN A2261 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN A2261 " 0.031 2.00e-02 2.50e+03 pdb=" N ALA A2262 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 849 " 0.032 2.00e-02 2.50e+03 3.13e-02 1.47e+01 pdb=" CG HIS A 849 " -0.067 2.00e-02 2.50e+03 pdb=" ND1 HIS A 849 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 849 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 849 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 849 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 590 " -0.019 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A 590 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 590 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 590 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 590 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 590 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 590 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 590 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 590 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 590 " -0.003 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 144 2.58 - 3.16: 12378 3.16 - 3.74: 22093 3.74 - 4.32: 30083 4.32 - 4.90: 49162 Nonbonded interactions: 113860 Sorted by model distance: nonbonded pdb=" CB HIS A2101 " pdb="ZN ZN A2405 " model vdw 1.995 2.104 nonbonded pdb=" CD2 HIS A 849 " pdb="ZN ZN A2403 " model vdw 2.183 2.450 nonbonded pdb=" O GLU A2259 " pdb=" CG1 ILE A2263 " model vdw 2.221 3.440 nonbonded pdb=" O LEU A 405 " pdb=" OG1 THR A 419 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A1134 " pdb=" NH1 ARG A1137 " model vdw 2.258 3.120 ... (remaining 113855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.000 Set scattering table: 0.090 Process input model: 40.130 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.008 0.084 14788 Z= 0.534 Angle : 1.016 14.329 20010 Z= 0.561 Chirality : 0.058 0.401 2233 Planarity : 0.006 0.058 2590 Dihedral : 14.995 88.687 5551 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.18), residues: 1808 helix: -1.25 (0.18), residues: 658 sheet: -1.51 (0.31), residues: 247 loop : -2.30 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 590 HIS 0.031 0.003 HIS A 849 PHE 0.048 0.003 PHE A2243 TYR 0.031 0.003 TYR A 522 ARG 0.020 0.001 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: A 1866 MET cc_start: 0.6642 (ptt) cc_final: 0.6404 (ptt) outliers start: 6 outliers final: 4 residues processed: 150 average time/residue: 0.3002 time to fit residues: 66.4935 Evaluate side-chains 113 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1130 ARG Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 2263 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A1342 ASN A1785 GLN ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2105 HIS ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14788 Z= 0.288 Angle : 0.703 11.415 20010 Z= 0.364 Chirality : 0.044 0.168 2233 Planarity : 0.005 0.062 2590 Dihedral : 6.101 53.495 1989 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.21 % Allowed : 9.10 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 1808 helix: -0.82 (0.19), residues: 681 sheet: -1.29 (0.31), residues: 245 loop : -2.13 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1574 HIS 0.021 0.001 HIS A 849 PHE 0.023 0.002 PHE A2210 TYR 0.022 0.002 TYR A 522 ARG 0.009 0.001 ARG A2109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 482 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7319 (m110) REVERT: A 1579 GLN cc_start: 0.6986 (tm-30) cc_final: 0.6580 (tm-30) outliers start: 19 outliers final: 12 residues processed: 141 average time/residue: 0.3138 time to fit residues: 65.0742 Evaluate side-chains 122 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 2160 ILE Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 166 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A1395 ASN A1785 GLN ** A1842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 HIS ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2211 GLN ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14788 Z= 0.336 Angle : 0.684 10.325 20010 Z= 0.353 Chirality : 0.044 0.158 2233 Planarity : 0.005 0.058 2590 Dihedral : 5.826 54.636 1981 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.29 % Allowed : 13.61 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 1808 helix: -0.67 (0.19), residues: 685 sheet: -1.18 (0.31), residues: 238 loop : -2.10 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1574 HIS 0.020 0.001 HIS A 849 PHE 0.018 0.002 PHE A2210 TYR 0.014 0.002 TYR A 421 ARG 0.008 0.000 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.840 Fit side-chains REVERT: A 373 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: A 482 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.7346 (m-40) REVERT: A 849 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.6113 (p-80) REVERT: A 1579 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 2128 ARG cc_start: 0.6846 (tpp80) cc_final: 0.6387 (mmp80) outliers start: 36 outliers final: 18 residues processed: 143 average time/residue: 0.2697 time to fit residues: 58.6774 Evaluate side-chains 129 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2160 ILE Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 20.0000 chunk 125 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 ASN A1785 GLN ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14788 Z= 0.267 Angle : 0.636 9.342 20010 Z= 0.328 Chirality : 0.043 0.171 2233 Planarity : 0.005 0.057 2590 Dihedral : 5.623 58.458 1981 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.74 % Allowed : 15.90 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1808 helix: -0.42 (0.19), residues: 682 sheet: -1.03 (0.32), residues: 238 loop : -1.98 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1574 HIS 0.018 0.001 HIS A 849 PHE 0.018 0.002 PHE A2210 TYR 0.012 0.002 TYR A 513 ARG 0.009 0.000 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: A 849 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.5916 (p-80) REVERT: A 1588 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 1775 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6107 (mm-30) REVERT: A 2109 ARG cc_start: 0.7515 (ptp90) cc_final: 0.7209 (ptp90) REVERT: A 2128 ARG cc_start: 0.6845 (tpp80) cc_final: 0.6322 (mmp80) outliers start: 43 outliers final: 25 residues processed: 153 average time/residue: 0.2849 time to fit residues: 64.7893 Evaluate side-chains 143 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1798 PHE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2160 ILE Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN A1785 GLN ** A1842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14788 Z= 0.256 Angle : 0.633 13.111 20010 Z= 0.323 Chirality : 0.043 0.195 2233 Planarity : 0.005 0.056 2590 Dihedral : 5.472 57.335 1981 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.12 % Allowed : 17.75 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1808 helix: -0.34 (0.19), residues: 682 sheet: -0.91 (0.32), residues: 238 loop : -1.91 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1574 HIS 0.017 0.001 HIS A 849 PHE 0.019 0.002 PHE A1304 TYR 0.013 0.002 TYR A 421 ARG 0.010 0.000 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 849 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.5877 (p-80) REVERT: A 851 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: A 914 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 1455 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7107 (tmm) REVERT: A 1588 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 1775 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6109 (mm-30) REVERT: A 2109 ARG cc_start: 0.7421 (ptp90) cc_final: 0.7129 (ptp90) REVERT: A 2128 ARG cc_start: 0.6797 (tpp80) cc_final: 0.6270 (mmp80) outliers start: 49 outliers final: 31 residues processed: 161 average time/residue: 0.2849 time to fit residues: 68.1575 Evaluate side-chains 153 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1134 GLU Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1455 MET Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1798 PHE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2160 ILE Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.0770 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 HIS A1785 GLN ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2211 GLN ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14788 Z= 0.377 Angle : 0.697 10.885 20010 Z= 0.353 Chirality : 0.045 0.251 2233 Planarity : 0.005 0.057 2590 Dihedral : 5.620 53.327 1981 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.82 % Allowed : 18.64 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1808 helix: -0.41 (0.19), residues: 683 sheet: -1.03 (0.31), residues: 244 loop : -1.95 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1574 HIS 0.020 0.001 HIS A 849 PHE 0.017 0.002 PHE A2210 TYR 0.017 0.002 TYR A 421 ARG 0.010 0.001 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: A 849 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.6014 (p-80) REVERT: A 851 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: A 914 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 1106 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 1455 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7102 (tmm) REVERT: A 1579 GLN cc_start: 0.6790 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 1588 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 1775 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6329 (mm-30) REVERT: A 2109 ARG cc_start: 0.7452 (ptp90) cc_final: 0.7205 (ptp90) outliers start: 60 outliers final: 38 residues processed: 160 average time/residue: 0.2822 time to fit residues: 67.5910 Evaluate side-chains 155 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1134 GLU Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1399 GLU Chi-restraints excluded: chain A residue 1455 MET Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1798 PHE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2160 ILE Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 GLN ** A1842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14788 Z= 0.187 Angle : 0.617 13.387 20010 Z= 0.309 Chirality : 0.042 0.171 2233 Planarity : 0.004 0.056 2590 Dihedral : 5.165 48.518 1981 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.05 % Allowed : 19.97 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1808 helix: -0.03 (0.20), residues: 681 sheet: -0.67 (0.32), residues: 238 loop : -1.80 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1956 HIS 0.012 0.001 HIS A 849 PHE 0.019 0.001 PHE A2210 TYR 0.012 0.001 TYR A 522 ARG 0.011 0.000 ARG A1100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: A 849 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.5801 (p-80) REVERT: A 851 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: A 1106 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6808 (t80) REVERT: A 1455 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: A 1531 MET cc_start: 0.7391 (mmm) cc_final: 0.6581 (mmm) REVERT: A 1588 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 1775 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6131 (mm-30) REVERT: A 1946 SER cc_start: 0.8947 (t) cc_final: 0.8697 (t) REVERT: A 2037 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 2166 ASN cc_start: 0.7454 (t0) cc_final: 0.7203 (t0) outliers start: 48 outliers final: 33 residues processed: 164 average time/residue: 0.3062 time to fit residues: 74.2557 Evaluate side-chains 155 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1134 GLU Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1455 MET Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1798 PHE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1870 LYS Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1269 HIS A1785 GLN ** A1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14788 Z= 0.177 Angle : 0.616 11.933 20010 Z= 0.310 Chirality : 0.041 0.188 2233 Planarity : 0.005 0.068 2590 Dihedral : 4.953 45.307 1981 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.99 % Allowed : 20.23 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1808 helix: 0.15 (0.20), residues: 680 sheet: -0.47 (0.32), residues: 238 loop : -1.73 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 550 HIS 0.011 0.001 HIS A 849 PHE 0.017 0.001 PHE A2210 TYR 0.011 0.001 TYR A 522 ARG 0.013 0.000 ARG A2109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 2.874 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 849 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.5793 (p-80) REVERT: A 851 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7332 (m-10) REVERT: A 1106 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 1455 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7006 (tmm) REVERT: A 1531 MET cc_start: 0.7301 (mmm) cc_final: 0.6424 (mmm) REVERT: A 1588 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7988 (tt) REVERT: A 1775 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: A 1946 SER cc_start: 0.8933 (t) cc_final: 0.8728 (t) REVERT: A 2166 ASN cc_start: 0.7435 (t0) cc_final: 0.7189 (t0) outliers start: 47 outliers final: 34 residues processed: 167 average time/residue: 0.2926 time to fit residues: 72.8202 Evaluate side-chains 156 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 849 HIS Chi-restraints excluded: chain A residue 851 TYR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1003 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1363 ILE Chi-restraints excluded: chain A residue 1399 GLU Chi-restraints excluded: chain A residue 1455 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1588 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1798 PHE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1861 LEU Chi-restraints excluded: chain A residue 1870 LYS Chi-restraints excluded: chain A residue 1904 CYS Chi-restraints excluded: chain A residue 2013 SER Chi-restraints excluded: chain A residue 2169 VAL Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 148 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: