Starting phenix.real_space_refine on Sat Sep 12 11:13:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxh_70981/09_2026/9oxh_70981.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 91 5.16 5 C 9481 2.51 5 N 2525 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14798 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 13766 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1765, 13757 Classifications: {'peptide': 1765} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 76, 'TRANS': 1688} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLN:plan1': 7, 'GLU:plan': 11, 'ARG:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 173 Conformer: "B" Number of residues, atoms: 1765, 13757 Classifications: {'peptide': 1765} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 76, 'TRANS': 1688} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLN:plan1': 7, 'GLU:plan': 11, 'ARG:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 173 bond proxies already assigned to first conformer: 14006 Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1003 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A2178 " occ=0.44 ... (16 atoms not shown) pdb=" NE2BGLN A2178 " occ=0.56 Time building chain proxies: 5.44, per 1000 atoms: 0.37 Number of scatterers: 14798 At special positions: 0 Unit cell: (101.915, 120.615, 160.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 2 15.00 Mg 1 11.99 O 2698 8.00 N 2525 7.00 C 9481 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: 1.30 Conformation dependent library (CDL) restraints added in 907.9 milliseconds 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 35.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.890A pdb=" N CYS A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 Processing helix chain 'A' and resid 605 through 613 removed outlier: 4.039A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 641 through 659 removed outlier: 4.176A pdb=" N GLN A 645 " --> pdb=" O VAL A 641 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 removed outlier: 4.119A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.644A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 703 Processing helix chain 'A' and resid 705 through 717 Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.973A pdb=" N GLU A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS A 727 " --> pdb=" O ILE A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 767 through 781 removed outlier: 4.235A pdb=" N GLY A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.513A pdb=" N ARG A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 833 through 846 removed outlier: 3.664A pdb=" N LEU A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 removed outlier: 3.701A pdb=" N GLU A1011 " --> pdb=" O SER A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.654A pdb=" N CYS A1031 " --> pdb=" O PRO A1027 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A1032 " --> pdb=" O GLN A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1057 removed outlier: 3.734A pdb=" N MET A1057 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1241 through 1245 removed outlier: 3.546A pdb=" N TRP A1244 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.643A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.524A pdb=" N LYS A1290 " --> pdb=" O GLU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1328 Processing helix chain 'A' and resid 1346 through 1355 removed outlier: 3.556A pdb=" N GLN A1353 " --> pdb=" O THR A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 4.321A pdb=" N PHE A1408 " --> pdb=" O THR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1465 through 1474 removed outlier: 3.956A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.976A pdb=" N ASP A1515 " --> pdb=" O LYS A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1538 removed outlier: 3.599A pdb=" N ARG A1538 " --> pdb=" O ILE A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1541 No H-bonds generated for 'chain 'A' and resid 1539 through 1541' Processing helix chain 'A' and resid 1550 through 1560 Processing helix chain 'A' and resid 1568 through 1579 removed outlier: 3.899A pdb=" N ALA A1572 " --> pdb=" O GLU A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1607 removed outlier: 3.640A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1654 removed outlier: 3.848A pdb=" N PHE A1650 " --> pdb=" O MET A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1714 removed outlier: 3.509A pdb=" N ARG A1707 " --> pdb=" O GLY A1703 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE A1709 " --> pdb=" O TRP A1705 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A1714 " --> pdb=" O ASN A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1792 Processing helix chain 'A' and resid 1828 through 1834 Processing helix chain 'A' and resid 1853 through 1855 No H-bonds generated for 'chain 'A' and resid 1853 through 1855' Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.562A pdb=" N ILE A1868 " --> pdb=" O PRO A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1871 through 1875 Processing helix chain 'A' and resid 1913 through 1926 removed outlier: 3.981A pdb=" N HIS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1986 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2040 through 2046 Processing helix chain 'A' and resid 2051 through 2068 removed outlier: 4.132A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2077 Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 3.890A pdb=" N LEU A2086 " --> pdb=" O GLU A2082 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2100 removed outlier: 4.096A pdb=" N GLU A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A2099 " --> pdb=" O PRO A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2115 removed outlier: 3.789A pdb=" N LEU A2110 " --> pdb=" O MET A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.196A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2134 through 2139' Processing helix chain 'A' and resid 2173 through 2176 removed outlier: 3.886A pdb=" N ARG A2176 " --> pdb=" O HIS A2173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2173 through 2176' Processing helix chain 'A' and resid 2278 through 2282 removed outlier: 3.931A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2397 Processing helix chain 'A' and resid 2431 through 2433 No H-bonds generated for 'chain 'A' and resid 2431 through 2433' Processing helix chain 'A' and resid 2499 through 2527 removed outlier: 3.693A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A2509 " --> pdb=" O GLN A2505 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A2525 " --> pdb=" O MET A2521 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A2526 " --> pdb=" O ARG A2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 28 through 36 removed outlier: 4.372A pdb=" N ARG B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.180A pdb=" N ASP B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.528A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A1040 " --> pdb=" O ASP A1064 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 7.049A pdb=" N PHE A1158 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1329 through 1331 Processing sheet with id=AA4, first strand: chain 'A' and resid 1372 through 1379 removed outlier: 3.988A pdb=" N ASP A1394 " --> pdb=" O ASP A1372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1388 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET A1335 " --> pdb=" O ASN A1391 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N TRP A1393 " --> pdb=" O MET A1335 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A1337 " --> pdb=" O TRP A1393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1450 through 1451 Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA7, first strand: chain 'A' and resid 1730 through 1731 removed outlier: 5.074A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A1764 " --> pdb=" O GLY A1751 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A1693 " --> pdb=" O ILE A1765 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1840 through 1841 removed outlier: 3.544A pdb=" N VAL A1841 " --> pdb=" O ILE A1850 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1896 through 1898 removed outlier: 3.733A pdb=" N ALA A1904 " --> pdb=" O MET A1947 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AB2, first strand: chain 'A' and resid 2140 through 2142 removed outlier: 6.737A pdb=" N VAL A2495 " --> pdb=" O THR A2141 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A2470 " --> pdb=" O TRP A2496 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A2473 " --> pdb=" O VAL A2457 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A2457 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 6.512A pdb=" N GLY A2170 " --> pdb=" O GLU A2153 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET A2155 " --> pdb=" O TRP A2168 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP A2168 " --> pdb=" O MET A2155 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A2169 " --> pdb=" O SER A2180 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A2181 " --> pdb=" O THR A2190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2199 through 2205 removed outlier: 4.026A pdb=" N CYS A2201 " --> pdb=" O GLY A2218 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP A2214 " --> pdb=" O VAL A2205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2223 through 2225 removed outlier: 4.862A pdb=" N LEU A2224 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2249 Processing sheet with id=AB7, first strand: chain 'A' and resid 2300 through 2303 removed outlier: 4.244A pdb=" N CYS A2302 " --> pdb=" O GLY A2318 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A2318 " --> pdb=" O CYS A2302 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A2324 " --> pdb=" O GLY A2317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.701A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A2385 " --> pdb=" O VAL A2375 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 7.014A pdb=" N LEU A2436 " --> pdb=" O ILE A2445 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1290 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: 3.39 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4793 1.34 - 1.46: 3061 1.46 - 1.58: 7086 1.58 - 1.70: 3 1.70 - 1.82: 136 Bond restraints: 15079 Sorted by residual: bond pdb=" C5 GDP A2602 " pdb=" C4 GDP A2602 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C5 GDP A2602 " pdb=" C6 GDP A2602 " ideal model delta sigma weight residual 1.490 1.410 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C6 GDP A2602 " pdb=" N1 GDP A2602 " ideal model delta sigma weight residual 1.337 1.391 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" N VAL A2396 " pdb=" CA VAL A2396 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.28e-02 6.10e+03 6.93e+00 bond pdb=" C8 GDP A2602 " pdb=" N7 GDP A2602 " ideal model delta sigma weight residual 1.350 1.307 0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 15074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 19999 2.87 - 5.73: 386 5.73 - 8.60: 49 8.60 - 11.47: 15 11.47 - 14.33: 3 Bond angle restraints: 20452 Sorted by residual: angle pdb=" C LYS A1316 " pdb=" N ASP A1317 " pdb=" CA ASP A1317 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C LEU A1955 " pdb=" N ASP A1956 " pdb=" CA ASP A1956 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C VAL A2048 " pdb=" N ILE A2049 " pdb=" CA ILE A2049 " ideal model delta sigma weight residual 121.97 129.61 -7.64 1.80e+00 3.09e-01 1.80e+01 angle pdb=" N ASP A2329 " pdb=" CA ASP A2329 " pdb=" C ASP A2329 " ideal model delta sigma weight residual 114.16 107.98 6.18 1.48e+00 4.57e-01 1.74e+01 angle pdb=" CA LEU A1042 " pdb=" CB LEU A1042 " pdb=" CG LEU A1042 " ideal model delta sigma weight residual 116.30 130.63 -14.33 3.50e+00 8.16e-02 1.68e+01 ... (remaining 20447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 8399 20.24 - 40.48: 648 40.48 - 60.72: 72 60.72 - 80.97: 10 80.97 - 101.21: 4 Dihedral angle restraints: 9133 sinusoidal: 3554 harmonic: 5579 Sorted by residual: dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual -180.00 -107.07 -72.93 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA SER A2327 " pdb=" C SER A2327 " pdb=" N ASN A2328 " pdb=" CA ASN A2328 " ideal model delta harmonic sigma weight residual -180.00 -135.92 -44.08 0 5.00e+00 4.00e-02 7.77e+01 dihedral pdb=" CA ALA A2268 " pdb=" C ALA A2268 " pdb=" N ASP A2269 " pdb=" CA ASP A2269 " ideal model delta harmonic sigma weight residual 180.00 137.33 42.67 0 5.00e+00 4.00e-02 7.28e+01 ... (remaining 9130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1955 0.063 - 0.127: 402 0.127 - 0.190: 40 0.190 - 0.253: 8 0.253 - 0.317: 2 Chirality restraints: 2407 Sorted by residual: chirality pdb=" CB ILE A2434 " pdb=" CA ILE A2434 " pdb=" CG1 ILE A2434 " pdb=" CG2 ILE A2434 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE A1990 " pdb=" CA ILE A1990 " pdb=" CG1 ILE A1990 " pdb=" CG2 ILE A1990 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PRO A1942 " pdb=" N PRO A1942 " pdb=" C PRO A1942 " pdb=" CB PRO A1942 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2404 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1317 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASP A1317 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP A1317 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A1318 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.064 5.00e-02 4.00e+02 9.89e-02 1.57e+01 pdb=" N PRO A1942 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A2094 " 0.063 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A2095 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A2095 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A2095 " 0.052 5.00e-02 4.00e+02 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 84 2.55 - 3.14: 11246 3.14 - 3.73: 22095 3.73 - 4.31: 30710 4.31 - 4.90: 51428 Nonbonded interactions: 115563 Sorted by model distance: nonbonded pdb="MG MG A2601 " pdb=" O2B GDP A2602 " model vdw 1.963 2.170 nonbonded pdb=" OG1 THR A1348 " pdb="MG MG A2601 " model vdw 2.049 2.170 nonbonded pdb=" OG1 THR A1368 " pdb="MG MG A2601 " model vdw 2.069 2.170 nonbonded pdb=" O TYR A1718 " pdb=" NE2 GLN A1779 " model vdw 2.236 3.120 nonbonded pdb=" O VAL A 748 " pdb=" OG SER A 753 " model vdw 2.262 3.040 ... (remaining 115558 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 ========== 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=0.44 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: 8.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.004 0.117 15079 Z= 0.203 Angle : 0.957 14.332 20452 Z= 0.476 Chirality : 0.053 0.317 2407 Planarity : 0.008 0.099 2579 Dihedral : 13.919 101.208 5497 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.96 % Favored : 88.35 % Rotamer: Outliers : 0.13 % Allowed : 0.44 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.18), residues: 1883 helix: -1.28 (0.19), residues: 619 sheet: -2.35 (0.32), residues: 274 loop : -2.48 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 637 TYR 0.038 0.002 TYR A1718 PHE 0.028 0.002 PHE A2326 TRP 0.020 0.002 TRP A1393 HIS 0.020 0.002 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (15079) covalent geometry : angle 0.95670 / 0.48 (20452) hydrogen bonds : bond 0.16599 / 10.82 ( 458) hydrogen bonds : angle 7.29151 / 5.08 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.570 Fit side-chains REVERT: A 1288 MET cc_start: 0.8756 (mtt) cc_final: 0.8319 (mtt) REVERT: A 1658 ILE cc_start: 0.6096 (mm) cc_final: 0.5699 (mm) REVERT: A 2169 LEU cc_start: 0.8384 (mp) cc_final: 0.8040 (mp) REVERT: A 2493 LEU cc_start: 0.7993 (tt) cc_final: 0.7741 (tp) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1055 time to fit residues: 35.8197 Evaluate side-chains 181 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS A2173 HIS ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.196526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.158556 restraints weight = 36728.304| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.79 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15079 Z= 0.151 Angle : 0.724 11.913 20452 Z= 0.362 Chirality : 0.046 0.226 2407 Planarity : 0.006 0.086 2579 Dihedral : 6.527 94.479 2025 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.53 % Favored : 88.78 % Rotamer: Outliers : 0.69 % Allowed : 7.41 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.18), residues: 1883 helix: -0.66 (0.20), residues: 614 sheet: -2.17 (0.30), residues: 293 loop : -2.41 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 637 TYR 0.026 0.002 TYR A1718 PHE 0.035 0.002 PHE A2079 TRP 0.020 0.002 TRP A2426 HIS 0.016 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15079) covalent geometry : angle 0.72401 / 0.36 (20452) hydrogen bonds : bond 0.04067 / 2.73 ( 458) hydrogen bonds : angle 5.59440 / 3.86 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 1658 ILE cc_start: 0.6015 (mm) cc_final: 0.5633 (mm) REVERT: A 1732 MET cc_start: 0.7439 (tmm) cc_final: 0.7088 (tmm) REVERT: A 2408 MET cc_start: 0.4180 (pmm) cc_final: 0.2511 (tmm) outliers start: 10 outliers final: 10 residues processed: 188 average time/residue: 0.1085 time to fit residues: 31.9803 Evaluate side-chains 176 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2202 LEU Chi-restraints excluded: chain A residue 2350 SER Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 91 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.0020 chunk 95 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1029 GLN A1068 ASN A1854 GLN ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.194597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.158557 restraints weight = 32097.826| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 3.31 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15079 Z= 0.154 Angle : 0.709 12.252 20452 Z= 0.352 Chirality : 0.045 0.231 2407 Planarity : 0.006 0.078 2579 Dihedral : 6.369 94.092 2025 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.59 % Favored : 88.72 % Rotamer: Outliers : 1.26 % Allowed : 9.86 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.19), residues: 1883 helix: -0.41 (0.21), residues: 621 sheet: -2.08 (0.30), residues: 291 loop : -2.39 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 637 TYR 0.032 0.002 TYR A1718 PHE 0.017 0.002 PHE A2326 TRP 0.019 0.002 TRP A2426 HIS 0.017 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (15079) covalent geometry : angle 0.70949 / 0.35 (20452) hydrogen bonds : bond 0.03573 / 2.38 ( 458) hydrogen bonds : angle 5.19915 / 3.58 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 1288 MET cc_start: 0.8308 (mtt) cc_final: 0.7925 (mtt) REVERT: A 1658 ILE cc_start: 0.6053 (mm) cc_final: 0.5566 (mm) REVERT: A 1696 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: A 1719 MET cc_start: 0.3186 (pmm) cc_final: 0.2841 (ptp) REVERT: A 1732 MET cc_start: 0.7398 (tmm) cc_final: 0.7061 (tmm) REVERT: A 2169 LEU cc_start: 0.8374 (mp) cc_final: 0.7986 (mp) REVERT: A 2408 MET cc_start: 0.3890 (pmm) cc_final: 0.2415 (tmm) outliers start: 19 outliers final: 15 residues processed: 192 average time/residue: 0.0960 time to fit residues: 29.5012 Evaluate side-chains 184 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1696 GLU Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2350 SER Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 152 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 57 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.196970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.152460 restraints weight = 27637.305| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.84 r_work: 0.3694 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15079 Z= 0.117 Angle : 0.652 11.246 20452 Z= 0.326 Chirality : 0.044 0.236 2407 Planarity : 0.005 0.069 2579 Dihedral : 6.106 86.587 2025 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.11 % Favored : 89.20 % Rotamer: Outliers : 1.26 % Allowed : 11.24 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.19), residues: 1883 helix: -0.14 (0.21), residues: 620 sheet: -1.93 (0.31), residues: 289 loop : -2.32 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1282 TYR 0.024 0.001 TYR A1718 PHE 0.024 0.001 PHE A2079 TRP 0.013 0.001 TRP A1393 HIS 0.012 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15079) covalent geometry : angle 0.65210 / 0.33 (20452) hydrogen bonds : bond 0.03094 / 2.07 ( 458) hydrogen bonds : angle 4.94698 / 3.40 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.574 Fit side-chains REVERT: A 743 SER cc_start: 0.7490 (m) cc_final: 0.7240 (p) REVERT: A 1466 MET cc_start: 0.8072 (mmp) cc_final: 0.7642 (mmt) REVERT: A 1658 ILE cc_start: 0.5998 (mm) cc_final: 0.5776 (mm) REVERT: A 1719 MET cc_start: 0.3406 (pmm) cc_final: 0.3177 (ptp) REVERT: A 1732 MET cc_start: 0.7883 (tmm) cc_final: 0.7508 (tmm) REVERT: A 2169 LEU cc_start: 0.8427 (mp) cc_final: 0.8038 (mp) REVERT: A 2363 LEU cc_start: 0.8346 (pp) cc_final: 0.8107 (pp) REVERT: A 2408 MET cc_start: 0.4309 (pmm) cc_final: 0.2670 (tmm) REVERT: A 2444 LEU cc_start: 0.8828 (tp) cc_final: 0.8540 (tp) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.1066 time to fit residues: 33.0515 Evaluate side-chains 181 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2217 SER Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 119 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.190340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151956 restraints weight = 34939.605| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.60 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15079 Z= 0.209 Angle : 0.745 14.284 20452 Z= 0.370 Chirality : 0.047 0.270 2407 Planarity : 0.005 0.073 2579 Dihedral : 6.460 93.433 2025 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.69 % Allowed : 11.44 % Favored : 87.87 % Rotamer: Outliers : 1.76 % Allowed : 12.30 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.19), residues: 1883 helix: -0.28 (0.21), residues: 629 sheet: -2.10 (0.30), residues: 293 loop : -2.31 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2122 TYR 0.040 0.002 TYR A1718 PHE 0.025 0.002 PHE A2079 TRP 0.021 0.002 TRP A2426 HIS 0.021 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (15079) covalent geometry : angle 0.74451 / 0.37 (20452) hydrogen bonds : bond 0.03556 / 2.41 ( 458) hydrogen bonds : angle 5.02775 / 3.47 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1658 ILE cc_start: 0.6158 (mm) cc_final: 0.5951 (mm) REVERT: A 1719 MET cc_start: 0.3085 (pmm) cc_final: 0.2383 (ptp) REVERT: A 1732 MET cc_start: 0.7498 (tmm) cc_final: 0.7052 (tmm) REVERT: A 1733 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7463 (p90) REVERT: A 2408 MET cc_start: 0.4301 (pmm) cc_final: 0.3000 (tmm) REVERT: A 2444 LEU cc_start: 0.8815 (tp) cc_final: 0.8534 (tp) outliers start: 27 outliers final: 21 residues processed: 191 average time/residue: 0.1029 time to fit residues: 31.9311 Evaluate side-chains 194 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1917 LEU Chi-restraints excluded: chain A residue 1980 ASP Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2217 SER Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2434 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 179 optimal weight: 0.0040 chunk 46 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 182 optimal weight: 0.0670 chunk 129 optimal weight: 1.9990 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1094 GLN A1779 GLN A2292 ASN ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.195455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150937 restraints weight = 27046.666| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.66 r_work: 0.3683 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15079 Z= 0.114 Angle : 0.655 12.650 20452 Z= 0.326 Chirality : 0.043 0.259 2407 Planarity : 0.005 0.064 2579 Dihedral : 6.062 83.221 2025 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.79 % Favored : 89.57 % Rotamer: Outliers : 1.44 % Allowed : 13.43 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.19), residues: 1883 helix: 0.08 (0.21), residues: 619 sheet: -1.93 (0.31), residues: 297 loop : -2.20 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1282 TYR 0.023 0.001 TYR A1718 PHE 0.020 0.001 PHE A2079 TRP 0.015 0.001 TRP A1734 HIS 0.011 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (15079) covalent geometry : angle 0.65509 / 0.33 (20452) hydrogen bonds : bond 0.02993 / 2.01 ( 458) hydrogen bonds : angle 4.81632 / 3.30 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1288 MET cc_start: 0.8427 (mtt) cc_final: 0.8108 (mtt) REVERT: A 1466 MET cc_start: 0.8191 (mmp) cc_final: 0.7818 (mmt) REVERT: A 1719 MET cc_start: 0.3201 (pmm) cc_final: 0.2635 (ptp) REVERT: A 1732 MET cc_start: 0.7942 (tmm) cc_final: 0.7609 (tmm) REVERT: A 2169 LEU cc_start: 0.8434 (mp) cc_final: 0.8030 (mp) REVERT: A 2408 MET cc_start: 0.4439 (pmm) cc_final: 0.2823 (tmm) REVERT: A 2444 LEU cc_start: 0.8948 (tp) cc_final: 0.8609 (tp) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 0.1099 time to fit residues: 34.4936 Evaluate side-chains 188 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 2048 VAL Chi-restraints excluded: chain A residue 2069 THR Chi-restraints excluded: chain A residue 2217 SER Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 153 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1779 GLN ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.192223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147642 restraints weight = 26939.113| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.49 r_work: 0.3633 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15079 Z= 0.156 Angle : 0.690 12.266 20452 Z= 0.343 Chirality : 0.045 0.266 2407 Planarity : 0.005 0.067 2579 Dihedral : 6.144 84.795 2025 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.85 % Favored : 88.46 % Rotamer: Outliers : 1.82 % Allowed : 13.87 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.19), residues: 1883 helix: -0.01 (0.21), residues: 628 sheet: -1.98 (0.31), residues: 291 loop : -2.23 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1282 TYR 0.031 0.002 TYR A1718 PHE 0.020 0.002 PHE A2079 TRP 0.016 0.002 TRP A1393 HIS 0.015 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (15079) covalent geometry : angle 0.69043 / 0.34 (20452) hydrogen bonds : bond 0.03172 / 2.16 ( 458) hydrogen bonds : angle 4.84380 / 3.33 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 743 SER cc_start: 0.7852 (p) cc_final: 0.7610 (m) REVERT: A 1575 PHE cc_start: 0.8166 (t80) cc_final: 0.7875 (t80) REVERT: A 1732 MET cc_start: 0.8011 (tmm) cc_final: 0.7579 (tmm) REVERT: A 1733 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7430 (p90) REVERT: A 2169 LEU cc_start: 0.8452 (mp) cc_final: 0.8034 (mp) REVERT: A 2408 MET cc_start: 0.4357 (pmm) cc_final: 0.2884 (tmm) REVERT: A 2444 LEU cc_start: 0.8937 (tp) cc_final: 0.8567 (tp) outliers start: 28 outliers final: 22 residues processed: 191 average time/residue: 0.1017 time to fit residues: 31.3778 Evaluate side-chains 197 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 992 ASN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1259 GLU Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1388 LEU Chi-restraints excluded: chain A residue 1429 ASP Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 2048 VAL Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2217 SER Chi-restraints excluded: chain A residue 2301 MET Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 6.9990 chunk 175 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 116 optimal weight: 0.0060 chunk 179 optimal weight: 0.0980 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0370 chunk 67 optimal weight: 0.0020 chunk 97 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1779 GLN ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.196694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158900 restraints weight = 28952.389| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.29 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15079 Z= 0.109 Angle : 0.651 15.027 20452 Z= 0.323 Chirality : 0.044 0.281 2407 Planarity : 0.005 0.061 2579 Dihedral : 5.852 71.600 2025 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.99 % Favored : 90.32 % Rotamer: Outliers : 1.19 % Allowed : 14.94 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % 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: -1.93 (0.19), residues: 1883 helix: 0.27 (0.22), residues: 615 sheet: -1.85 (0.31), residues: 297 loop : -2.17 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1282 TYR 0.026 0.001 TYR A1718 PHE 0.023 0.001 PHE A2079 TRP 0.016 0.001 TRP A1734 HIS 0.009 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (15079) covalent geometry : angle 0.65134 / 0.32 (20452) hydrogen bonds : bond 0.02868 / 1.93 ( 458) hydrogen bonds : angle 4.74676 / 3.26 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 MET cc_start: 0.7302 (tmm) cc_final: 0.7050 (tmm) REVERT: A 1733 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7042 (p90) REVERT: A 2408 MET cc_start: 0.4145 (pmm) cc_final: 0.2764 (tmm) outliers start: 18 outliers final: 16 residues processed: 191 average time/residue: 0.0991 time to fit residues: 30.5356 Evaluate side-chains 186 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 2048 VAL Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 21 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.0040 chunk 89 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.2350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.196390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156282 restraints weight = 35811.177| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.75 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15079 Z= 0.111 Angle : 0.651 14.338 20452 Z= 0.323 Chirality : 0.043 0.271 2407 Planarity : 0.005 0.062 2579 Dihedral : 5.715 70.331 2025 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.63 % Favored : 89.68 % Rotamer: Outliers : 1.13 % Allowed : 15.25 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.17 % 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: -1.91 (0.19), residues: 1883 helix: 0.30 (0.22), residues: 620 sheet: -1.83 (0.31), residues: 296 loop : -2.18 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1282 TYR 0.025 0.001 TYR A1718 PHE 0.022 0.001 PHE A2079 TRP 0.013 0.001 TRP A1734 HIS 0.017 0.001 HIS A1310 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15079) covalent geometry : angle 0.65108 / 0.32 (20452) hydrogen bonds : bond 0.02851 / 1.92 ( 458) hydrogen bonds : angle 4.71402 / 3.25 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 1466 MET cc_start: 0.7630 (mmp) cc_final: 0.7364 (mmt) REVERT: A 1732 MET cc_start: 0.7258 (tmm) cc_final: 0.7007 (tmm) REVERT: A 1733 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 2075 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 2408 MET cc_start: 0.3944 (pmm) cc_final: 0.2570 (tmm) outliers start: 17 outliers final: 16 residues processed: 192 average time/residue: 0.0997 time to fit residues: 31.1982 Evaluate side-chains 191 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 2048 VAL Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 135 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 187 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.196501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158394 restraints weight = 36026.853| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.79 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15079 Z= 0.116 Angle : 0.657 14.363 20452 Z= 0.325 Chirality : 0.044 0.279 2407 Planarity : 0.005 0.062 2579 Dihedral : 5.695 70.154 2025 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.89 % Favored : 89.47 % Rotamer: Outliers : 1.19 % Allowed : 15.76 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.22 % 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: -1.87 (0.19), residues: 1883 helix: 0.31 (0.22), residues: 620 sheet: -1.83 (0.31), residues: 295 loop : -2.14 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1282 TYR 0.026 0.001 TYR A1718 PHE 0.026 0.001 PHE A2079 TRP 0.012 0.001 TRP A1734 HIS 0.009 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15079) covalent geometry : angle 0.65670 / 0.33 (20452) hydrogen bonds : bond 0.02880 / 1.94 ( 458) hydrogen bonds : angle 4.70987 / 3.25 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3766 Ramachandran restraints generated. 1883 Oldfield, 0 Emsley, 1883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 1336 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7021 (ptpt) REVERT: A 1466 MET cc_start: 0.7541 (mmp) cc_final: 0.7292 (mmt) REVERT: A 1732 MET cc_start: 0.7260 (tmm) cc_final: 0.6994 (tmm) REVERT: A 1733 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7052 (p90) REVERT: A 2408 MET cc_start: 0.4009 (pmm) cc_final: 0.2598 (tmm) outliers start: 18 outliers final: 15 residues processed: 186 average time/residue: 0.0973 time to fit residues: 29.4191 Evaluate side-chains 188 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1234 ILE Chi-restraints excluded: chain A residue 1336 LYS Chi-restraints excluded: chain A residue 1378 ILE Chi-restraints excluded: chain A residue 1529 GLU Chi-restraints excluded: chain A residue 1733 TYR Chi-restraints excluded: chain A residue 1754 VAL Chi-restraints excluded: chain A residue 1767 VAL Chi-restraints excluded: chain A residue 1870 LEU Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 2048 VAL Chi-restraints excluded: chain A residue 2356 THR Chi-restraints excluded: chain A residue 2435 LEU Chi-restraints excluded: chain A residue 2460 THR Chi-restraints excluded: chain B residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1779 GLN A1871 ASN ** A2391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147067 restraints weight = 24617.768| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.22 r_work: 0.3635 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15079 Z= 0.167 Angle : 0.720 14.445 20452 Z= 0.356 Chirality : 0.046 0.279 2407 Planarity : 0.005 0.065 2579 Dihedral : 6.011 75.913 2025 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.74 % Favored : 88.62 % Rotamer: Outliers : 1.38 % Allowed : 15.76 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % Twisted General : 0.11 % 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: -1.98 (0.19), residues: 1883 helix: 0.16 (0.22), residues: 621 sheet: -1.94 (0.31), residues: 296 loop : -2.14 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2122 TYR 0.037 0.002 TYR A1718 PHE 0.022 0.002 PHE A2079 TRP 0.015 0.002 TRP A2426 HIS 0.014 0.001 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (15079) covalent geometry : angle 0.71968 / 0.36 (20452) hydrogen bonds : bond 0.03233 / 2.19 ( 458) hydrogen bonds : angle 4.83626 / 3.35 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3547.06 seconds wall clock time: 61 minutes 42.20 seconds (3702.20 seconds total)