Starting phenix.real_space_refine on Sun Aug 9 15:19:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yno_73219/08_2026/9yno_73219.map" } resolution = 4.06 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= 0.003 sd= 0.007 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 P 18 5.49 5 S 124 5.16 5 C 21392 2.51 5 N 6370 2.21 5 O 6680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34590 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 15856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2102, 15856 Classifications: {'peptide': 2102} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 2039} Chain breaks: 19 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1290 Unresolved non-hydrogen angles: 1674 Unresolved non-hydrogen dihedrals: 1072 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'TYR:plan': 16, 'HIS:plan': 7, 'GLU:plan': 17, 'ASN:plan1': 18, 'ASP:plan': 18, 'ARG:plan': 19, 'PHE:plan': 33, 'TRP:plan': 4, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 672 Chain: "B" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1572, 7801 Classifications: {'peptide': 1572} Incomplete info: {'truncation_to_alanine': 1439} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1528} Chain breaks: 14 Unresolved chain link angles: 43 Unresolved non-hydrogen bonds: 5262 Unresolved non-hydrogen angles: 6733 Unresolved non-hydrogen dihedrals: 4349 Unresolved non-hydrogen chiralities: 505 Planarities with less than four sites: {'ARG:plan': 80, 'PHE:plan': 86, 'ASP:plan': 80, 'TYR:plan': 59, 'ASN:plan1': 91, 'GLN:plan1': 68, 'GLU:plan': 111, 'TRP:plan': 11, 'HIS:plan': 44} Unresolved non-hydrogen planarities: 2877 Chain: "C" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 2080 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 382} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 408} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1456 Unresolved non-hydrogen angles: 1879 Unresolved non-hydrogen dihedrals: 1220 Unresolved non-hydrogen chiralities: 147 Planarities with less than four sites: {'TYR:plan': 19, 'ASN:plan1': 20, 'HIS:plan': 8, 'GLN:plan1': 9, 'GLU:plan': 25, 'ARG:plan': 25, 'ASP:plan': 20, 'PHE:plan': 34, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 803 Chain: "D" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 2035 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 374} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 399} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1424 Unresolved non-hydrogen angles: 1838 Unresolved non-hydrogen dihedrals: 1191 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'ASN:plan1': 20, 'HIS:plan': 8, 'GLN:plan1': 9, 'GLU:plan': 25, 'ARG:plan': 25, 'ASP:plan': 20, 'PHE:plan': 34, 'TYR:plan': 17, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 789 Chain: "E" Number of atoms: 6640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6640 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 26, 'TRANS': 794} Chain breaks: 7 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'I3P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15237 SG CYS A2562 82.667 53.281 81.604 1.00 70.08 S ATOM 15262 SG CYS A2565 83.729 56.527 80.992 1.00 65.30 S Time building chain proxies: 7.44, per 1000 atoms: 0.22 Number of scatterers: 34590 At special positions: 0 Unit cell: (146.316, 206.322, 234.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 124 16.00 P 18 15.00 O 6680 8.00 N 6370 7.00 C 21392 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: 2.93 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2803 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A2587 " pdb="ZN ZN A2803 " - pdb=" NE2 HIS A2582 " pdb="ZN ZN A2803 " - pdb=" SG CYS A2562 " pdb="ZN ZN A2803 " - pdb=" SG CYS A2565 " Number of angles added : 2 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10228 Finding SS restraints... Secondary structure from input PDB file: 278 helices and 21 sheets defined 68.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 78 Processing helix chain 'A' and resid 87 through 110 removed outlier: 3.705A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.717A pdb=" N ALA A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.911A pdb=" N VAL A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 removed outlier: 3.757A pdb=" N LYS A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.736A pdb=" N ASP A 495 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.590A pdb=" N GLN A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.709A pdb=" N LEU A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY A 542 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 543 " --> pdb=" O ASP A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 564 removed outlier: 3.694A pdb=" N LYS A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 577 through 584 removed outlier: 3.816A pdb=" N MET A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 611 through 625 removed outlier: 3.677A pdb=" N ILE A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 4.475A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 632 " --> pdb=" O PRO A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.554A pdb=" N LEU A 665 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 removed outlier: 3.535A pdb=" N GLY A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 741 Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.610A pdb=" N ASP A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 786 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.733A pdb=" N ILE A 807 " --> pdb=" O TRP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 819 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.567A pdb=" N ARG A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 removed outlier: 4.015A pdb=" N MET A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 873 removed outlier: 3.819A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.299A pdb=" N ARG A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 1000 removed outlier: 3.658A pdb=" N PHE A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1035 Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.719A pdb=" N GLY A1075 " --> pdb=" O PRO A1071 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1105 through 1125 Processing helix chain 'A' and resid 1126 through 1129 Processing helix chain 'A' and resid 1174 through 1194 removed outlier: 3.508A pdb=" N TYR A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1201 removed outlier: 3.791A pdb=" N ASN A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.560A pdb=" N ASN A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1222 removed outlier: 3.785A pdb=" N VAL A1215 " --> pdb=" O GLY A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1246 removed outlier: 3.703A pdb=" N GLU A1233 " --> pdb=" O GLU A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 Processing helix chain 'A' and resid 1259 through 1264 removed outlier: 3.500A pdb=" N LEU A1262 " --> pdb=" O HIS A1259 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A1263 " --> pdb=" O LEU A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1279 Processing helix chain 'A' and resid 1281 through 1286 removed outlier: 3.852A pdb=" N CYS A1285 " --> pdb=" O ASN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1303 removed outlier: 4.102A pdb=" N VAL A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1316 removed outlier: 4.095A pdb=" N LEU A1310 " --> pdb=" O HIS A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1338 Processing helix chain 'A' and resid 1351 through 1360 Processing helix chain 'A' and resid 1371 through 1385 Processing helix chain 'A' and resid 1390 through 1401 removed outlier: 3.780A pdb=" N LYS A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1412 Processing helix chain 'A' and resid 1416 through 1430 Processing helix chain 'A' and resid 1447 through 1459 Processing helix chain 'A' and resid 1475 through 1491 removed outlier: 4.018A pdb=" N VAL A1479 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET A1484 " --> pdb=" O THR A1480 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A1488 " --> pdb=" O MET A1484 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1520 Processing helix chain 'A' and resid 1603 through 1624 Proline residue: A1619 - end of helix removed outlier: 3.531A pdb=" N GLN A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1634 removed outlier: 3.985A pdb=" N LEU A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1629 " --> pdb=" O PHE A1625 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A1630 " --> pdb=" O SER A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1649 Processing helix chain 'A' and resid 1651 through 1662 removed outlier: 3.646A pdb=" N LYS A1662 " --> pdb=" O ASN A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1684 Processing helix chain 'A' and resid 1689 through 1704 removed outlier: 3.587A pdb=" N ARG A1696 " --> pdb=" O GLY A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1752 Processing helix chain 'A' and resid 1753 through 1765 Processing helix chain 'A' and resid 1767 through 1783 Processing helix chain 'A' and resid 1786 through 1801 removed outlier: 3.685A pdb=" N LYS A1801 " --> pdb=" O LEU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1824 removed outlier: 3.765A pdb=" N THR A1824 " --> pdb=" O GLU A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1917 Processing helix chain 'A' and resid 1917 through 1930 removed outlier: 3.621A pdb=" N ILE A1921 " --> pdb=" O ILE A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1942 removed outlier: 3.612A pdb=" N ARG A1941 " --> pdb=" O GLN A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1963 Processing helix chain 'A' and resid 1964 through 1969 Processing helix chain 'A' and resid 1972 through 1977 Processing helix chain 'A' and resid 1981 through 1997 Processing helix chain 'A' and resid 2002 through 2009 Processing helix chain 'A' and resid 2014 through 2024 Processing helix chain 'A' and resid 2026 through 2031 Processing helix chain 'A' and resid 2033 through 2052 removed outlier: 4.274A pdb=" N VAL A2037 " --> pdb=" O ARG A2033 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A2052 " --> pdb=" O LEU A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2058 through 2066 Processing helix chain 'A' and resid 2069 through 2086 removed outlier: 3.755A pdb=" N LEU A2073 " --> pdb=" O ARG A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2100 through 2117 removed outlier: 3.511A pdb=" N VAL A2104 " --> pdb=" O SER A2100 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A2117 " --> pdb=" O HIS A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2119 through 2126 removed outlier: 3.631A pdb=" N GLN A2123 " --> pdb=" O ASN A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2145 Processing helix chain 'A' and resid 2167 through 2172 Processing helix chain 'A' and resid 2173 through 2183 Processing helix chain 'A' and resid 2192 through 2216 removed outlier: 3.699A pdb=" N PHE A2196 " --> pdb=" O LYS A2192 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A2202 " --> pdb=" O GLN A2198 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2225 removed outlier: 3.551A pdb=" N HIS A2225 " --> pdb=" O TRP A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2248 removed outlier: 3.684A pdb=" N TRP A2229 " --> pdb=" O HIS A2225 " (cutoff:3.500A) Processing helix chain 'A' and resid 2288 through 2301 Processing helix chain 'A' and resid 2305 through 2331 Processing helix chain 'A' and resid 2332 through 2335 removed outlier: 3.706A pdb=" N ARG A2335 " --> pdb=" O THR A2332 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2335' Processing helix chain 'A' and resid 2336 through 2343 Processing helix chain 'A' and resid 2343 through 2362 Processing helix chain 'A' and resid 2363 through 2366 removed outlier: 3.544A pdb=" N PHE A2366 " --> pdb=" O HIS A2363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2363 through 2366' Processing helix chain 'A' and resid 2367 through 2372 removed outlier: 3.667A pdb=" N LEU A2371 " --> pdb=" O TYR A2367 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A2372 " --> pdb=" O SER A2368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2367 through 2372' Processing helix chain 'A' and resid 2372 through 2378 removed outlier: 3.936A pdb=" N TYR A2376 " --> pdb=" O PHE A2372 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2390 removed outlier: 3.782A pdb=" N VAL A2388 " --> pdb=" O VAL A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2416 Processing helix chain 'A' and resid 2417 through 2420 Processing helix chain 'A' and resid 2481 through 2495 Processing helix chain 'A' and resid 2498 through 2503 removed outlier: 3.733A pdb=" N GLY A2501 " --> pdb=" O GLY A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2513 through 2528 Processing helix chain 'A' and resid 2531 through 2560 Processing helix chain 'A' and resid 2569 through 2573 removed outlier: 3.555A pdb=" N ASP A2573 " --> pdb=" O ASP A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2578 through 2586 Processing helix chain 'A' and resid 2588 through 2601 Processing helix chain 'A' and resid 2608 through 2620 Processing helix chain 'A' and resid 2631 through 2635 removed outlier: 3.880A pdb=" N VAL A2635 " --> pdb=" O MET A2632 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 709 through 719 Processing helix chain 'B' and resid 720 through 741 Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 757 through 766 Processing helix chain 'B' and resid 771 through 787 removed outlier: 3.973A pdb=" N VAL B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 removed outlier: 3.996A pdb=" N THR B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 829 removed outlier: 3.630A pdb=" N MET B 827 " --> pdb=" O SER B 823 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 847 removed outlier: 3.819A pdb=" N GLU B 836 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 874 Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.794A pdb=" N ARG B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 1000 Processing helix chain 'B' and resid 1027 through 1038 Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1069 through 1085 removed outlier: 3.963A pdb=" N GLY B1075 " --> pdb=" O PRO B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1096 Processing helix chain 'B' and resid 1102 through 1125 Processing helix chain 'B' and resid 1126 through 1130 Processing helix chain 'B' and resid 1175 through 1194 Processing helix chain 'B' and resid 1196 through 1210 removed outlier: 3.761A pdb=" N ASN B1201 " --> pdb=" O LYS B1197 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B1202 " --> pdb=" O LYS B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1222 removed outlier: 3.733A pdb=" N VAL B1215 " --> pdb=" O GLY B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1246 Processing helix chain 'B' and resid 1249 through 1258 Processing helix chain 'B' and resid 1259 through 1264 removed outlier: 4.209A pdb=" N PHE B1263 " --> pdb=" O HIS B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1267 through 1278 Processing helix chain 'B' and resid 1281 through 1287 Processing helix chain 'B' and resid 1289 through 1304 removed outlier: 3.815A pdb=" N VAL B1293 " --> pdb=" O SER B1289 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B1304 " --> pdb=" O ILE B1300 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1317 removed outlier: 3.522A pdb=" N LEU B1310 " --> pdb=" O HIS B1306 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B1317 " --> pdb=" O LEU B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1338 Processing helix chain 'B' and resid 1338 through 1343 removed outlier: 3.715A pdb=" N VAL B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B1343 " --> pdb=" O GLY B1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1338 through 1343' Processing helix chain 'B' and resid 1351 through 1361 Processing helix chain 'B' and resid 1370 through 1386 Processing helix chain 'B' and resid 1390 through 1401 removed outlier: 3.543A pdb=" N SER B1399 " --> pdb=" O ILE B1395 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1411 Processing helix chain 'B' and resid 1416 through 1431 Processing helix chain 'B' and resid 1446 through 1461 Processing helix chain 'B' and resid 1474 through 1493 removed outlier: 4.714A pdb=" N ILE B1483 " --> pdb=" O VAL B1479 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N MET B1484 " --> pdb=" O THR B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1497 removed outlier: 3.636A pdb=" N ASP B1497 " --> pdb=" O PRO B1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1494 through 1497' Processing helix chain 'B' and resid 1502 through 1504 No H-bonds generated for 'chain 'B' and resid 1502 through 1504' Processing helix chain 'B' and resid 1505 through 1520 removed outlier: 3.663A pdb=" N PHE B1509 " --> pdb=" O HIS B1505 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B1510 " --> pdb=" O GLN B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1544 removed outlier: 4.181A pdb=" N SER B1532 " --> pdb=" O ALA B1528 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B1533 " --> pdb=" O GLN B1529 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B1539 " --> pdb=" O SER B1535 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B1542 " --> pdb=" O ARG B1538 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B1543 " --> pdb=" O THR B1539 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1634 Proline residue: B1619 - end of helix Processing helix chain 'B' and resid 1635 through 1638 Processing helix chain 'B' and resid 1643 through 1649 Processing helix chain 'B' and resid 1651 through 1664 removed outlier: 3.687A pdb=" N LYS B1662 " --> pdb=" O ASN B1658 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B1664 " --> pdb=" O THR B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1667 through 1684 Processing helix chain 'B' and resid 1689 through 1705 Processing helix chain 'B' and resid 1741 through 1752 Processing helix chain 'B' and resid 1753 through 1764 Processing helix chain 'B' and resid 1767 through 1783 Processing helix chain 'B' and resid 1786 through 1799 Processing helix chain 'B' and resid 1802 through 1824 removed outlier: 3.523A pdb=" N PHE B1806 " --> pdb=" O LYS B1802 " (cutoff:3.500A) Processing helix chain 'B' and resid 1912 through 1929 removed outlier: 3.692A pdb=" N MET B1918 " --> pdb=" O ALA B1914 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B1919 " --> pdb=" O ILE B1915 " (cutoff:3.500A) Proline residue: B1920 - end of helix removed outlier: 3.688A pdb=" N CYS B1929 " --> pdb=" O LEU B1925 " (cutoff:3.500A) Processing helix chain 'B' and resid 1930 through 1932 No H-bonds generated for 'chain 'B' and resid 1930 through 1932' Processing helix chain 'B' and resid 1933 through 1943 Processing helix chain 'B' and resid 1950 through 1963 removed outlier: 3.517A pdb=" N CYS B1963 " --> pdb=" O LEU B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1966 through 1970 removed outlier: 3.576A pdb=" N LEU B1970 " --> pdb=" O THR B1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1971 through 1975 removed outlier: 4.241A pdb=" N GLY B1974 " --> pdb=" O GLY B1971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1998 removed outlier: 3.505A pdb=" N VAL B1985 " --> pdb=" O ASN B1981 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B1998 " --> pdb=" O GLU B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2009 removed outlier: 3.656A pdb=" N CYS B2006 " --> pdb=" O GLU B2002 " (cutoff:3.500A) Processing helix chain 'B' and resid 2013 through 2024 Processing helix chain 'B' and resid 2026 through 2033 removed outlier: 3.713A pdb=" N TYR B2032 " --> pdb=" O PRO B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2033 through 2052 removed outlier: 4.281A pdb=" N VAL B2037 " --> pdb=" O ARG B2033 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B2052 " --> pdb=" O LEU B2048 " (cutoff:3.500A) Processing helix chain 'B' and resid 2058 through 2066 Processing helix chain 'B' and resid 2069 through 2087 Processing helix chain 'B' and resid 2100 through 2116 removed outlier: 3.631A pdb=" N VAL B2104 " --> pdb=" O SER B2100 " (cutoff:3.500A) Processing helix chain 'B' and resid 2119 through 2126 removed outlier: 3.597A pdb=" N GLN B2123 " --> pdb=" O ASN B2119 " (cutoff:3.500A) Processing helix chain 'B' and resid 2137 through 2145 Processing helix chain 'B' and resid 2168 through 2172 Processing helix chain 'B' and resid 2173 through 2183 Processing helix chain 'B' and resid 2192 through 2216 removed outlier: 4.658A pdb=" N GLU B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B2202 " --> pdb=" O GLN B2198 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) Processing helix chain 'B' and resid 2216 through 2225 removed outlier: 3.568A pdb=" N HIS B2225 " --> pdb=" O TRP B2221 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2248 Processing helix chain 'B' and resid 2288 through 2302 Processing helix chain 'B' and resid 2305 through 2331 Processing helix chain 'B' and resid 2336 through 2343 Processing helix chain 'B' and resid 2343 through 2362 Processing helix chain 'B' and resid 2364 through 2371 Processing helix chain 'B' and resid 2372 through 2378 removed outlier: 3.813A pdb=" N TYR B2376 " --> pdb=" O PHE B2372 " (cutoff:3.500A) Processing helix chain 'B' and resid 2378 through 2390 removed outlier: 3.888A pdb=" N VAL B2388 " --> pdb=" O VAL B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2391 through 2416 Processing helix chain 'B' and resid 2417 through 2421 removed outlier: 3.631A pdb=" N PHE B2421 " --> pdb=" O LYS B2418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2494 Processing helix chain 'B' and resid 2499 through 2503 removed outlier: 3.570A pdb=" N VAL B2503 " --> pdb=" O VAL B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2513 through 2528 Processing helix chain 'B' and resid 2531 through 2561 Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 3.945A pdb=" N PHE B2572 " --> pdb=" O GLU B2568 " (cutoff:3.500A) Processing helix chain 'B' and resid 2578 through 2585 Processing helix chain 'B' and resid 2588 through 2602 Processing helix chain 'B' and resid 2603 through 2607 removed outlier: 3.607A pdb=" N TYR B2607 " --> pdb=" O PRO B2604 " (cutoff:3.500A) Processing helix chain 'B' and resid 2608 through 2620 Processing helix chain 'B' and resid 2622 through 2626 removed outlier: 4.120A pdb=" N TRP B2625 " --> pdb=" O ASN B2622 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B2626 " --> pdb=" O LEU B2623 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2622 through 2626' Processing helix chain 'C' and resid 2140 through 2144 Processing helix chain 'C' and resid 2166 through 2172 Processing helix chain 'C' and resid 2173 through 2184 removed outlier: 3.672A pdb=" N THR C2184 " --> pdb=" O VAL C2180 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2214 removed outlier: 4.397A pdb=" N GLU C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP C2202 " --> pdb=" O GLN C2198 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C2214 " --> pdb=" O GLN C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2216 through 2225 removed outlier: 3.565A pdb=" N PHE C2220 " --> pdb=" O ASN C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2226 through 2248 Processing helix chain 'C' and resid 2288 through 2303 Processing helix chain 'C' and resid 2305 through 2331 Processing helix chain 'C' and resid 2336 through 2343 Processing helix chain 'C' and resid 2343 through 2362 Processing helix chain 'C' and resid 2363 through 2371 Processing helix chain 'C' and resid 2372 through 2378 removed outlier: 3.785A pdb=" N TYR C2376 " --> pdb=" O PHE C2372 " (cutoff:3.500A) Processing helix chain 'C' and resid 2378 through 2390 removed outlier: 3.720A pdb=" N VAL C2388 " --> pdb=" O VAL C2384 " (cutoff:3.500A) Processing helix chain 'C' and resid 2391 through 2417 removed outlier: 3.501A pdb=" N ILE C2395 " --> pdb=" O ASN C2391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2481 through 2496 removed outlier: 3.661A pdb=" N ARG C2495 " --> pdb=" O ASN C2491 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2503 Processing helix chain 'C' and resid 2513 through 2528 Processing helix chain 'C' and resid 2532 through 2561 removed outlier: 4.104A pdb=" N PHE C2537 " --> pdb=" O LEU C2533 " (cutoff:3.500A) Processing helix chain 'C' and resid 2568 through 2573 Processing helix chain 'C' and resid 2578 through 2585 Processing helix chain 'C' and resid 2588 through 2601 Processing helix chain 'C' and resid 2608 through 2620 Processing helix chain 'D' and resid 2167 through 2172 Processing helix chain 'D' and resid 2173 through 2184 Processing helix chain 'D' and resid 2192 through 2214 removed outlier: 4.308A pdb=" N GLU D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP D2202 " --> pdb=" O GLN D2198 " (cutoff:3.500A) Processing helix chain 'D' and resid 2216 through 2225 Processing helix chain 'D' and resid 2225 through 2248 removed outlier: 3.519A pdb=" N TRP D2229 " --> pdb=" O HIS D2225 " (cutoff:3.500A) Processing helix chain 'D' and resid 2288 through 2302 Processing helix chain 'D' and resid 2305 through 2331 Processing helix chain 'D' and resid 2332 through 2335 Processing helix chain 'D' and resid 2336 through 2343 Processing helix chain 'D' and resid 2343 through 2361 Processing helix chain 'D' and resid 2363 through 2371 Processing helix chain 'D' and resid 2372 through 2377 removed outlier: 3.932A pdb=" N TYR D2376 " --> pdb=" O PHE D2372 " (cutoff:3.500A) Processing helix chain 'D' and resid 2378 through 2390 removed outlier: 3.574A pdb=" N VAL D2388 " --> pdb=" O VAL D2384 " (cutoff:3.500A) Processing helix chain 'D' and resid 2391 through 2416 removed outlier: 3.816A pdb=" N ILE D2395 " --> pdb=" O ASN D2391 " (cutoff:3.500A) Processing helix chain 'D' and resid 2481 through 2494 Processing helix chain 'D' and resid 2498 through 2502 removed outlier: 4.206A pdb=" N GLY D2501 " --> pdb=" O GLY D2498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2513 through 2528 Processing helix chain 'D' and resid 2532 through 2560 Processing helix chain 'D' and resid 2569 through 2573 Processing helix chain 'D' and resid 2578 through 2585 Processing helix chain 'D' and resid 2588 through 2601 Processing helix chain 'D' and resid 2602 through 2607 removed outlier: 6.194A pdb=" N THR D2605 " --> pdb=" O LYS D2602 " (cutoff:3.500A) Processing helix chain 'D' and resid 2608 through 2620 Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.549A pdb=" N LYS E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 159 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 435 through 462 removed outlier: 3.744A pdb=" N VAL E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 485 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 513 through 524 Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 546 through 564 removed outlier: 3.620A pdb=" N LYS E 550 " --> pdb=" O TYR E 546 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR E 551 " --> pdb=" O ALA E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 576 Processing helix chain 'E' and resid 577 through 584 removed outlier: 3.702A pdb=" N MET E 581 " --> pdb=" O ASN E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 599 Processing helix chain 'E' and resid 602 through 610 Processing helix chain 'E' and resid 611 through 625 removed outlier: 3.507A pdb=" N ILE E 615 " --> pdb=" O THR E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 638 Processing helix chain 'E' and resid 645 through 657 Processing helix chain 'E' and resid 709 through 719 Processing helix chain 'E' and resid 721 through 740 removed outlier: 3.711A pdb=" N VAL E 726 " --> pdb=" O ALA E 722 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU E 727 " --> pdb=" O ASP E 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 757 through 767 Processing helix chain 'E' and resid 771 through 786 Processing helix chain 'E' and resid 821 through 829 removed outlier: 3.594A pdb=" N ASP E 826 " --> pdb=" O SER E 822 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET E 827 " --> pdb=" O SER E 823 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 829 " --> pdb=" O ASN E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 832 through 846 removed outlier: 3.908A pdb=" N GLU E 836 " --> pdb=" O ALA E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 857 through 875 Processing helix chain 'E' and resid 878 through 889 removed outlier: 3.819A pdb=" N ARG E 887 " --> pdb=" O LEU E 883 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 888 " --> pdb=" O ARG E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 964 through 987 removed outlier: 3.595A pdb=" N ASP E 986 " --> pdb=" O SER E 982 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 5.947A pdb=" N LEU A 17 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 27 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 26 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS A 40 " --> pdb=" O PHE A 26 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 40 current: chain 'A' and resid 122 through 125 removed outlier: 5.248A pdb=" N LEU A 123 " --> pdb=" O LEU A 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 148 through 152 current: chain 'A' and resid 181 through 185 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 181 through 185 current: chain 'A' and resid 207 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 244 removed outlier: 14.196A pdb=" N VAL A 240 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N CYS A 253 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A 242 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 250 " --> pdb=" O ARG A 265 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 265 current: chain 'A' and resid 303 through 307 removed outlier: 14.924A pdb=" N PHE A 303 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N ALA A 316 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE A 305 " --> pdb=" O LEU A 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 352 through 357 current: chain 'A' and resid 386 through 391 removed outlier: 15.592A pdb=" N VAL A 387 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N SER A 400 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 389 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 639 through 640 Processing sheet with id=AA4, first strand: chain 'A' and resid 667 through 672 Processing sheet with id=AA5, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AA6, first strand: chain 'A' and resid 2146 through 2152 Processing sheet with id=AA7, first strand: chain 'A' and resid 2422 through 2427 Processing sheet with id=AA8, first strand: chain 'B' and resid 639 through 640 removed outlier: 3.564A pdb=" N SER B 640 " --> pdb=" O THR B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 667 through 671 Processing sheet with id=AB1, first strand: chain 'B' and resid 1318 through 1319 removed outlier: 3.532A pdb=" N ALA B1319 " --> pdb=" O LYS B1322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2146 through 2152 Processing sheet with id=AB3, first strand: chain 'B' and resid 2423 through 2427 Processing sheet with id=AB4, first strand: chain 'C' and resid 2147 through 2152 Processing sheet with id=AB5, first strand: chain 'C' and resid 2422 through 2427 Processing sheet with id=AB6, first strand: chain 'D' and resid 2146 through 2152 Processing sheet with id=AB7, first strand: chain 'D' and resid 2422 through 2427 Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 152 removed outlier: 5.041A pdb=" N LEU E 123 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N VAL E 134 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N ILE E 121 " --> pdb=" O VAL E 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 29 removed outlier: 5.740A pdb=" N CYS E 37 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU E 208 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 239 through 244 removed outlier: 14.341A pdb=" N VAL E 240 " --> pdb=" O CYS E 253 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N CYS E 253 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU E 242 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE E 250 " --> pdb=" O ARG E 265 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 265 current: chain 'E' and resid 304 through 307 removed outlier: 5.330A pdb=" N PHE E 305 " --> pdb=" O LEU E 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 352 through 357 current: chain 'E' and resid 386 through 391 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 386 through 391 current: chain 'E' and resid 414 through 420 Processing sheet with id=AC2, first strand: chain 'E' and resid 639 through 640 Processing sheet with id=AC3, first strand: chain 'E' and resid 667 through 672 2568 hydrogen bonds defined for protein. 7386 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: 9.62 Time building geometry restraints manager: 3.87 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: 12362 1.34 - 1.46: 6117 1.46 - 1.58: 16238 1.58 - 1.70: 26 1.70 - 1.81: 192 Bond restraints: 34935 Sorted by residual: bond pdb=" SD MET A1274 " pdb=" CE MET A1274 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.63e+00 bond pdb=" CB PHE A 772 " pdb=" CG PHE A 772 " ideal model delta sigma weight residual 1.502 1.465 0.037 2.30e-02 1.89e+03 2.54e+00 bond pdb=" C ILE A 163 " pdb=" N HIS A 164 " ideal model delta sigma weight residual 1.333 1.368 -0.036 2.74e-02 1.33e+03 1.70e+00 bond pdb=" CD2 TYR A 117 " pdb=" CE2 TYR A 117 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CA LEU A1099 " pdb=" C LEU A1099 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.44e-02 4.82e+03 9.23e-01 ... (remaining 34930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 46552 1.22 - 2.44: 1015 2.44 - 3.67: 157 3.67 - 4.89: 35 4.89 - 6.11: 12 Bond angle restraints: 47771 Sorted by residual: angle pdb=" N VAL B1317 " pdb=" CA VAL B1317 " pdb=" C VAL B1317 " ideal model delta sigma weight residual 110.72 114.32 -3.60 1.01e+00 9.80e-01 1.27e+01 angle pdb=" N ILE E 752 " pdb=" CA ILE E 752 " pdb=" C ILE E 752 " ideal model delta sigma weight residual 112.96 109.41 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N VAL C2388 " pdb=" CA VAL C2388 " pdb=" C VAL C2388 " ideal model delta sigma weight residual 112.96 109.56 3.40 1.00e+00 1.00e+00 1.15e+01 angle pdb=" N ILE D2531 " pdb=" CA ILE D2531 " pdb=" C ILE D2531 " ideal model delta sigma weight residual 113.71 111.05 2.66 9.50e-01 1.11e+00 7.86e+00 angle pdb=" C HIS B 786 " pdb=" N VAL B 787 " pdb=" CA VAL B 787 " ideal model delta sigma weight residual 122.97 120.30 2.67 9.80e-01 1.04e+00 7.40e+00 ... (remaining 47766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 19543 17.67 - 35.34: 1293 35.34 - 53.01: 211 53.01 - 70.68: 48 70.68 - 88.35: 29 Dihedral angle restraints: 21124 sinusoidal: 5528 harmonic: 15596 Sorted by residual: dihedral pdb=" CA ASP A1026 " pdb=" C ASP A1026 " pdb=" N ILE A1027 " pdb=" CA ILE A1027 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASP A2136 " pdb=" C ASP A2136 " pdb=" N GLU A2137 " pdb=" CA GLU A2137 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG A 789 " pdb=" C ARG A 789 " pdb=" N ASP A 790 " pdb=" CA ASP A 790 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 21121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4184 0.039 - 0.077: 1389 0.077 - 0.116: 305 0.116 - 0.155: 22 0.155 - 0.194: 2 Chirality restraints: 5902 Sorted by residual: chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB ILE A 403 " pdb=" CA ILE A 403 " pdb=" CG1 ILE A 403 " pdb=" CG2 ILE A 403 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA GLU A 715 " pdb=" N GLU A 715 " pdb=" C GLU A 715 " pdb=" CB GLU A 715 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 5899 not shown) Planarity restraints: 6382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1069 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO A1070 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1070 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1070 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1265 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A1266 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1266 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1266 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1096 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLN A1096 " 0.024 2.00e-02 2.50e+03 pdb=" O GLN A1096 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A1097 " -0.008 2.00e-02 2.50e+03 ... (remaining 6379 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 148 2.68 - 3.24: 35027 3.24 - 3.79: 54215 3.79 - 4.35: 64006 4.35 - 4.90: 106774 Nonbonded interactions: 260170 Sorted by model distance: nonbonded pdb=" N CYS B2565 " pdb="ZN ZN B2802 " model vdw 2.127 2.310 nonbonded pdb=" O THR A2605 " pdb="CA CA A2804 " model vdw 2.234 2.510 nonbonded pdb=" OE1 GLU A1994 " pdb="CA CA A2804 " model vdw 2.243 2.510 nonbonded pdb=" OE2 GLU A1994 " pdb="CA CA A2804 " model vdw 2.291 2.510 nonbonded pdb=" CB HIS B2587 " pdb="ZN ZN B2802 " model vdw 2.427 2.630 ... (remaining 260165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2143 through 2630 or resid 2801 through 2802)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 38.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.002 0.058 34939 Z= 0.121 Angle : 0.467 18.820 47773 Z= 0.267 Chirality : 0.039 0.194 5902 Planarity : 0.003 0.047 6382 Dihedral : 13.292 88.355 10896 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.12), residues: 5228 helix: 2.15 (0.09), residues: 3247 sheet: -0.39 (0.27), residues: 394 loop : -0.55 (0.17), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1822 TYR 0.012 0.001 TYR A2204 PHE 0.020 0.001 PHE A 772 TRP 0.013 0.001 TRP A1129 HIS 0.013 0.001 HIS A1932 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (34935) covalent geometry : angle 0.45822 / 0.27 (47771) hydrogen bonds : bond 0.12229 / 8.04 ( 2568) hydrogen bonds : angle 5.12327 / 3.57 ( 7386) metal coordination : bond 0.03586 / 1.79 ( 4) metal coordination : angle 13.76988 / 8.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 152 ASP cc_start: 0.7256 (t70) cc_final: 0.6781 (t0) REVERT: A 185 MET cc_start: 0.8219 (tpp) cc_final: 0.7856 (mmm) REVERT: A 224 MET cc_start: 0.8307 (ttm) cc_final: 0.8051 (ttm) REVERT: A 289 HIS cc_start: 0.7189 (p-80) cc_final: 0.6915 (p90) REVERT: A 349 LYS cc_start: 0.8499 (ptpp) cc_final: 0.8259 (pttt) REVERT: A 388 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7752 (mtm-85) REVERT: A 414 MET cc_start: 0.7392 (ppp) cc_final: 0.7088 (ppp) REVERT: A 457 LYS cc_start: 0.8727 (tppt) cc_final: 0.8364 (tppt) REVERT: A 466 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 470 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7675 (ttp-110) REVERT: A 474 LYS cc_start: 0.8185 (tptp) cc_final: 0.7460 (tptt) REVERT: A 561 ARG cc_start: 0.7813 (ttt-90) cc_final: 0.7598 (ttt90) REVERT: A 699 ASP cc_start: 0.7160 (m-30) cc_final: 0.6591 (m-30) REVERT: A 703 GLU cc_start: 0.7893 (pm20) cc_final: 0.7355 (pm20) REVERT: A 705 HIS cc_start: 0.7976 (m90) cc_final: 0.7430 (m90) REVERT: A 782 MET cc_start: 0.8127 (tpp) cc_final: 0.7887 (tpp) REVERT: A 1094 PHE cc_start: 0.7874 (t80) cc_final: 0.7448 (t80) REVERT: A 1171 ILE cc_start: 0.8096 (mm) cc_final: 0.7871 (tp) REVERT: A 1210 MET cc_start: 0.8964 (mmp) cc_final: 0.8719 (mmm) REVERT: A 1227 ASN cc_start: 0.7724 (p0) cc_final: 0.7363 (p0) REVERT: A 1274 MET cc_start: 0.8548 (mmm) cc_final: 0.8317 (mmm) REVERT: A 1286 ASN cc_start: 0.8136 (t0) cc_final: 0.7768 (t0) REVERT: A 1343 LEU cc_start: 0.7873 (mt) cc_final: 0.7582 (pp) REVERT: A 1353 PRO cc_start: 0.8218 (Cg_exo) cc_final: 0.7856 (Cg_endo) REVERT: A 1632 LEU cc_start: 0.8754 (mt) cc_final: 0.8415 (mt) REVERT: A 1670 LEU cc_start: 0.8404 (mt) cc_final: 0.7921 (mt) REVERT: A 1684 LYS cc_start: 0.5775 (mtpp) cc_final: 0.5461 (tptt) REVERT: E 29 THR cc_start: 0.7848 (m) cc_final: 0.7513 (p) REVERT: E 65 ARG cc_start: 0.7574 (mpt90) cc_final: 0.7362 (mtt-85) REVERT: E 166 PHE cc_start: 0.7855 (t80) cc_final: 0.7643 (t80) REVERT: E 215 ASN cc_start: 0.7425 (p0) cc_final: 0.6885 (t0) REVERT: E 234 LEU cc_start: 0.8062 (mp) cc_final: 0.7740 (tt) REVERT: E 441 ASP cc_start: 0.6731 (m-30) cc_final: 0.6462 (m-30) REVERT: E 493 VAL cc_start: 0.8233 (m) cc_final: 0.7472 (p) REVERT: E 505 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7177 (mmt90) REVERT: E 693 VAL cc_start: 0.8637 (t) cc_final: 0.8261 (m) REVERT: E 740 MET cc_start: 0.7834 (ttm) cc_final: 0.7447 (ttp) REVERT: E 967 MET cc_start: 0.6792 (mtp) cc_final: 0.6562 (tpp) REVERT: E 977 LEU cc_start: 0.8518 (mt) cc_final: 0.8244 (pp) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2041 time to fit residues: 142.4911 Evaluate side-chains 308 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 50.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN A 602 ASN A1104 GLN A1203 HIS A1283 HIS ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1945 ASN ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.094505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082594 restraints weight = 155655.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081571 restraints weight = 198298.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082264 restraints weight = 180788.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082164 restraints weight = 117986.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082449 restraints weight = 107435.593| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 34939 Z= 0.358 Angle : 0.678 23.293 47773 Z= 0.362 Chirality : 0.045 0.262 5902 Planarity : 0.004 0.054 6382 Dihedral : 5.971 87.809 5708 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.17 % Allowed : 6.13 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.26 (0.12), residues: 5228 helix: 1.77 (0.09), residues: 3260 sheet: -0.65 (0.27), residues: 403 loop : -0.71 (0.17), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1311 TYR 0.032 0.002 TYR E 72 PHE 0.033 0.002 PHE A 831 TRP 0.013 0.002 TRP A1129 HIS 0.014 0.002 HIS A1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.36 (34935) covalent geometry : angle 0.66913 / 0.36 (47771) hydrogen bonds : bond 0.04438 / 2.96 ( 2568) hydrogen bonds : angle 4.68558 / 3.29 ( 7386) metal coordination : bond 0.04907 / 2.45 ( 4) metal coordination : angle 17.12544 / 10.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 362 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8478 (m) cc_final: 0.8105 (p) REVERT: A 185 MET cc_start: 0.8493 (tpp) cc_final: 0.8205 (mmm) REVERT: A 457 LYS cc_start: 0.8645 (tppt) cc_final: 0.8286 (tppt) REVERT: A 466 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7441 (tm-30) REVERT: A 470 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7757 (ttp-110) REVERT: A 703 GLU cc_start: 0.7806 (pm20) cc_final: 0.7501 (pm20) REVERT: A 715 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6732 (mm-30) REVERT: A 755 GLN cc_start: 0.7297 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 756 LEU cc_start: 0.8308 (mt) cc_final: 0.8005 (mt) REVERT: A 782 MET cc_start: 0.7933 (tpp) cc_final: 0.7715 (tpp) REVERT: A 1094 PHE cc_start: 0.7699 (t80) cc_final: 0.7352 (t80) REVERT: A 1210 MET cc_start: 0.9058 (mmp) cc_final: 0.8776 (mmm) REVERT: A 1227 ASN cc_start: 0.7424 (p0) cc_final: 0.6973 (p0) REVERT: A 1286 ASN cc_start: 0.7925 (t0) cc_final: 0.7576 (t0) REVERT: E 89 LEU cc_start: 0.8387 (tt) cc_final: 0.7817 (mt) REVERT: E 92 LEU cc_start: 0.8102 (tp) cc_final: 0.7677 (mt) REVERT: E 166 PHE cc_start: 0.8034 (t80) cc_final: 0.7770 (t80) REVERT: E 215 ASN cc_start: 0.7647 (p0) cc_final: 0.6954 (t0) REVERT: E 234 LEU cc_start: 0.8125 (mp) cc_final: 0.7775 (tt) REVERT: E 414 MET cc_start: 0.6978 (ppp) cc_final: 0.6708 (ppp) REVERT: E 693 VAL cc_start: 0.8776 (t) cc_final: 0.8344 (m) REVERT: E 710 ARG cc_start: 0.7722 (mtt90) cc_final: 0.7168 (mtt90) REVERT: E 723 ASP cc_start: 0.7397 (m-30) cc_final: 0.7172 (m-30) REVERT: E 740 MET cc_start: 0.7843 (ttm) cc_final: 0.7630 (ttp) REVERT: E 967 MET cc_start: 0.6782 (mtp) cc_final: 0.6492 (tpp) REVERT: E 977 LEU cc_start: 0.8494 (mt) cc_final: 0.8241 (pp) outliers start: 4 outliers final: 0 residues processed: 365 average time/residue: 0.2020 time to fit residues: 120.9961 Evaluate side-chains 300 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 131 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 294 optimal weight: 30.0000 chunk 258 optimal weight: 4.9990 chunk 451 optimal weight: 0.3980 chunk 346 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 GLN A 649 GLN A 745 GLN A1067 HIS ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1249 ASN ** A1943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.094363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082206 restraints weight = 145744.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080418 restraints weight = 148984.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081228 restraints weight = 123708.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.081307 restraints weight = 88769.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.081351 restraints weight = 84652.122| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34939 Z= 0.233 Angle : 0.560 22.995 47773 Z= 0.300 Chirality : 0.042 0.225 5902 Planarity : 0.003 0.056 6382 Dihedral : 5.747 89.771 5708 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.12), residues: 5228 helix: 1.94 (0.09), residues: 3271 sheet: -0.76 (0.26), residues: 409 loop : -0.73 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1247 TYR 0.026 0.002 TYR E 72 PHE 0.024 0.002 PHE A 778 TRP 0.011 0.001 TRP A1129 HIS 0.012 0.001 HIS A2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (34935) covalent geometry : angle 0.54988 / 0.30 (47771) hydrogen bonds : bond 0.03724 / 2.48 ( 2568) hydrogen bonds : angle 4.27856 / 3.00 ( 7386) metal coordination : bond 0.03586 / 1.79 ( 4) metal coordination : angle 16.74396 / 9.79 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 185 MET cc_start: 0.8434 (tpp) cc_final: 0.8120 (mmm) REVERT: A 352 TYR cc_start: 0.7096 (m-80) cc_final: 0.6871 (m-10) REVERT: A 450 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7898 (mtmm) REVERT: A 457 LYS cc_start: 0.8680 (tppt) cc_final: 0.8263 (tppt) REVERT: A 466 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 509 MET cc_start: 0.7784 (mmm) cc_final: 0.7502 (mmm) REVERT: A 715 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6887 (mm-30) REVERT: A 755 GLN cc_start: 0.7379 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 756 LEU cc_start: 0.8351 (mt) cc_final: 0.7920 (mt) REVERT: A 782 MET cc_start: 0.8014 (tpp) cc_final: 0.7783 (tpp) REVERT: A 1104 GLN cc_start: 0.7514 (tp-100) cc_final: 0.7288 (tp-100) REVERT: A 1210 MET cc_start: 0.8988 (mmp) cc_final: 0.8727 (mmm) REVERT: A 1227 ASN cc_start: 0.7330 (p0) cc_final: 0.6905 (p0) REVERT: A 1286 ASN cc_start: 0.8063 (t0) cc_final: 0.7728 (t0) REVERT: A 1956 LEU cc_start: 0.8275 (tp) cc_final: 0.8059 (tp) REVERT: E 166 PHE cc_start: 0.8083 (t80) cc_final: 0.7827 (t80) REVERT: E 215 ASN cc_start: 0.7698 (p0) cc_final: 0.6926 (t0) REVERT: E 234 LEU cc_start: 0.7997 (mp) cc_final: 0.7584 (tt) REVERT: E 414 MET cc_start: 0.6789 (ppp) cc_final: 0.6466 (ppp) REVERT: E 441 ASP cc_start: 0.7048 (m-30) cc_final: 0.6699 (m-30) REVERT: E 723 ASP cc_start: 0.7570 (m-30) cc_final: 0.7262 (m-30) REVERT: E 967 MET cc_start: 0.6934 (mtp) cc_final: 0.6543 (mmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2198 time to fit residues: 124.8164 Evaluate side-chains 291 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 426 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 464 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 404 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 HIS A1048 GLN A1104 GLN ** A1303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2113 HIS E 77 GLN ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.093996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081773 restraints weight = 154777.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079809 restraints weight = 178019.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080583 restraints weight = 155447.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080783 restraints weight = 106881.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080867 restraints weight = 103007.582| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 34939 Z= 0.406 Angle : 0.733 24.257 47773 Z= 0.390 Chirality : 0.047 0.295 5902 Planarity : 0.004 0.057 6382 Dihedral : 6.220 79.318 5708 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.12), residues: 5228 helix: 1.53 (0.09), residues: 3252 sheet: -0.87 (0.27), residues: 395 loop : -0.98 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1247 TYR 0.035 0.003 TYR A 800 PHE 0.032 0.003 PHE A 831 TRP 0.015 0.002 TRP A1129 HIS 0.015 0.002 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.41 (34935) covalent geometry : angle 0.72414 / 0.39 (47771) hydrogen bonds : bond 0.04625 / 3.09 ( 2568) hydrogen bonds : angle 4.81963 / 3.39 ( 7386) metal coordination : bond 0.04644 / 2.32 ( 4) metal coordination : angle 17.80434 / 10.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8470 (m) cc_final: 0.8113 (p) REVERT: A 70 LYS cc_start: 0.8702 (pttt) cc_final: 0.8435 (pttp) REVERT: A 93 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 450 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7894 (mtmm) REVERT: A 466 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 715 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6685 (mm-30) REVERT: A 756 LEU cc_start: 0.8457 (mt) cc_final: 0.7964 (mt) REVERT: A 1210 MET cc_start: 0.8983 (mmp) cc_final: 0.8656 (mmm) REVERT: A 1227 ASN cc_start: 0.7256 (p0) cc_final: 0.6788 (p0) REVERT: A 1297 VAL cc_start: 0.8896 (t) cc_final: 0.8611 (p) REVERT: A 1306 HIS cc_start: 0.7098 (m-70) cc_final: 0.6775 (m-70) REVERT: A 1340 GLU cc_start: 0.5602 (tp30) cc_final: 0.5267 (tp30) REVERT: A 2052 MET cc_start: 0.6803 (mtp) cc_final: 0.6509 (mtp) REVERT: E 166 PHE cc_start: 0.8089 (t80) cc_final: 0.7800 (t80) REVERT: E 185 MET cc_start: 0.7878 (tpp) cc_final: 0.7473 (tpt) REVERT: E 215 ASN cc_start: 0.7707 (p0) cc_final: 0.6970 (t0) REVERT: E 234 LEU cc_start: 0.8095 (mp) cc_final: 0.7762 (tt) REVERT: E 255 GLU cc_start: 0.8314 (tt0) cc_final: 0.7977 (tt0) REVERT: E 693 VAL cc_start: 0.8819 (t) cc_final: 0.8323 (m) REVERT: E 723 ASP cc_start: 0.7467 (m-30) cc_final: 0.7164 (m-30) REVERT: E 967 MET cc_start: 0.7030 (mtp) cc_final: 0.6170 (mmp) REVERT: E 977 LEU cc_start: 0.8458 (mt) cc_final: 0.8211 (pp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2149 time to fit residues: 123.0535 Evaluate side-chains 290 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 62 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 462 optimal weight: 0.3980 chunk 426 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 458 optimal weight: 10.0000 chunk 320 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1086 GLN ** A1943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2060 ASN ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 600 HIS ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.095934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084074 restraints weight = 155775.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083878 restraints weight = 176351.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084189 restraints weight = 154855.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084180 restraints weight = 99482.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.084430 restraints weight = 90640.751| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34939 Z= 0.180 Angle : 0.532 19.950 47773 Z= 0.287 Chirality : 0.041 0.170 5902 Planarity : 0.003 0.057 6382 Dihedral : 5.751 79.963 5708 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 5228 helix: 1.95 (0.09), residues: 3265 sheet: -0.94 (0.26), residues: 415 loop : -0.80 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1941 TYR 0.023 0.002 TYR E 256 PHE 0.034 0.002 PHE A2563 TRP 0.014 0.001 TRP A1129 HIS 0.009 0.001 HIS A2113 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (34935) covalent geometry : angle 0.52333 / 0.29 (47771) hydrogen bonds : bond 0.03514 / 2.34 ( 2568) hydrogen bonds : angle 4.15791 / 2.91 ( 7386) metal coordination : bond 0.03413 / 1.71 ( 4) metal coordination : angle 14.74923 / 8.60 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8460 (m) cc_final: 0.8096 (p) REVERT: A 48 ASN cc_start: 0.8386 (m110) cc_final: 0.8182 (m-40) REVERT: A 70 LYS cc_start: 0.8856 (pttt) cc_final: 0.8587 (pttm) REVERT: A 450 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7916 (mtmm) REVERT: A 466 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 715 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6631 (mm-30) REVERT: A 1210 MET cc_start: 0.8995 (mmp) cc_final: 0.8764 (mmm) REVERT: A 1227 ASN cc_start: 0.7368 (p0) cc_final: 0.6890 (p0) REVERT: A 1306 HIS cc_start: 0.7058 (m-70) cc_final: 0.6857 (m170) REVERT: A 1956 LEU cc_start: 0.8318 (tp) cc_final: 0.7988 (tp) REVERT: A 2052 MET cc_start: 0.6634 (mtp) cc_final: 0.6381 (mtp) REVERT: E 166 PHE cc_start: 0.7957 (t80) cc_final: 0.7749 (t80) REVERT: E 185 MET cc_start: 0.7810 (tpp) cc_final: 0.7448 (tpt) REVERT: E 215 ASN cc_start: 0.7626 (p0) cc_final: 0.6942 (t0) REVERT: E 234 LEU cc_start: 0.8223 (mp) cc_final: 0.7874 (tt) REVERT: E 414 MET cc_start: 0.7102 (ppp) cc_final: 0.6698 (ppp) REVERT: E 693 VAL cc_start: 0.8738 (t) cc_final: 0.8251 (m) REVERT: E 827 MET cc_start: 0.3636 (mtm) cc_final: 0.3402 (mtt) REVERT: E 967 MET cc_start: 0.6697 (mtp) cc_final: 0.6387 (tpp) outliers start: 2 outliers final: 1 residues processed: 325 average time/residue: 0.2119 time to fit residues: 115.8679 Evaluate side-chains 279 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 396 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 326 optimal weight: 20.0000 chunk 309 optimal weight: 30.0000 chunk 485 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 414 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 352 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 ASN A 577 ASN ** A1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 HIS ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2113 HIS ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 825 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.094473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082234 restraints weight = 155559.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.080428 restraints weight = 176186.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081171 restraints weight = 152080.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.081288 restraints weight = 107606.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081329 restraints weight = 103919.097| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 34939 Z= 0.334 Angle : 0.670 21.993 47773 Z= 0.358 Chirality : 0.045 0.211 5902 Planarity : 0.004 0.059 6382 Dihedral : 6.047 80.122 5708 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.08 (0.12), residues: 5228 helix: 1.73 (0.09), residues: 3257 sheet: -0.94 (0.27), residues: 410 loop : -0.95 (0.17), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1941 TYR 0.031 0.002 TYR A 800 PHE 0.035 0.002 PHE E 526 TRP 0.053 0.002 TRP E 694 HIS 0.013 0.002 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.33 (34935) covalent geometry : angle 0.66168 / 0.36 (47771) hydrogen bonds : bond 0.04217 / 2.81 ( 2568) hydrogen bonds : angle 4.54950 / 3.20 ( 7386) metal coordination : bond 0.04452 / 2.23 ( 4) metal coordination : angle 16.33209 / 9.52 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 TYR cc_start: 0.6713 (m-80) cc_final: 0.6430 (m-10) REVERT: A 70 LYS cc_start: 0.8823 (pttt) cc_final: 0.8569 (pttp) REVERT: A 466 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 655 PHE cc_start: 0.8107 (m-80) cc_final: 0.7901 (m-80) REVERT: A 715 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6592 (mm-30) REVERT: A 992 MET cc_start: 0.7142 (ttm) cc_final: 0.6928 (ttm) REVERT: A 1104 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7223 (tp-100) REVERT: A 1210 MET cc_start: 0.8988 (mmp) cc_final: 0.8666 (mmm) REVERT: A 1227 ASN cc_start: 0.7356 (p0) cc_final: 0.6735 (p0) REVERT: A 1306 HIS cc_start: 0.7110 (m-70) cc_final: 0.6787 (m-70) REVERT: E 166 PHE cc_start: 0.8073 (t80) cc_final: 0.7843 (t80) REVERT: E 185 MET cc_start: 0.7805 (tpp) cc_final: 0.7441 (tpt) REVERT: E 215 ASN cc_start: 0.7686 (p0) cc_final: 0.6962 (t0) REVERT: E 234 LEU cc_start: 0.8186 (mp) cc_final: 0.7769 (tt) REVERT: E 255 GLU cc_start: 0.8155 (tt0) cc_final: 0.7923 (tt0) REVERT: E 441 ASP cc_start: 0.6923 (m-30) cc_final: 0.6709 (m-30) REVERT: E 967 MET cc_start: 0.6908 (mtp) cc_final: 0.6483 (tpp) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.2108 time to fit residues: 115.5446 Evaluate side-chains 280 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 474 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 380 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 HIS A1067 HIS A1178 ASN A1948 ASN ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.095542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083742 restraints weight = 155344.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082656 restraints weight = 199243.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083370 restraints weight = 163500.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083645 restraints weight = 105871.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.083715 restraints weight = 108824.402| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34939 Z= 0.212 Angle : 0.563 23.687 47773 Z= 0.301 Chirality : 0.042 0.215 5902 Planarity : 0.003 0.057 6382 Dihedral : 5.831 80.796 5708 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 5228 helix: 1.92 (0.09), residues: 3271 sheet: -0.94 (0.26), residues: 416 loop : -0.85 (0.17), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1941 TYR 0.030 0.002 TYR E 256 PHE 0.027 0.002 PHE A 166 TRP 0.026 0.002 TRP E 694 HIS 0.010 0.001 HIS A2118 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (34935) covalent geometry : angle 0.55196 / 0.30 (47771) hydrogen bonds : bond 0.03612 / 2.41 ( 2568) hydrogen bonds : angle 4.20207 / 2.95 ( 7386) metal coordination : bond 0.02800 / 1.40 ( 4) metal coordination : angle 17.17790 / 10.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8907 (pttt) cc_final: 0.8596 (pttp) REVERT: A 450 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7817 (mtmm) REVERT: A 466 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 715 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 782 MET cc_start: 0.7984 (tpp) cc_final: 0.7686 (tpp) REVERT: A 1104 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7101 (tp-100) REVERT: A 1210 MET cc_start: 0.8941 (mmp) cc_final: 0.8603 (mmm) REVERT: A 1227 ASN cc_start: 0.7531 (p0) cc_final: 0.7065 (p0) REVERT: A 1340 GLU cc_start: 0.5301 (tp30) cc_final: 0.5073 (tp30) REVERT: E 166 PHE cc_start: 0.7940 (t80) cc_final: 0.7730 (t80) REVERT: E 185 MET cc_start: 0.7778 (tpp) cc_final: 0.7417 (tpt) REVERT: E 215 ASN cc_start: 0.7621 (p0) cc_final: 0.6940 (t0) REVERT: E 234 LEU cc_start: 0.8239 (mp) cc_final: 0.7974 (tt) REVERT: E 414 MET cc_start: 0.7080 (ppp) cc_final: 0.6741 (ppp) REVERT: E 441 ASP cc_start: 0.6896 (m-30) cc_final: 0.6591 (m-30) REVERT: E 967 MET cc_start: 0.6760 (mtp) cc_final: 0.6386 (tpp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2157 time to fit residues: 115.3864 Evaluate side-chains 273 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 214 optimal weight: 50.0000 chunk 139 optimal weight: 0.0770 chunk 423 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 519 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 407 optimal weight: 20.0000 chunk 507 optimal weight: 1.9990 chunk 257 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 261 HIS A 384 ASN ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084248 restraints weight = 155633.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083565 restraints weight = 178598.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084086 restraints weight = 161710.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084163 restraints weight = 100653.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084285 restraints weight = 95474.091| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34939 Z= 0.158 Angle : 0.516 20.138 47773 Z= 0.277 Chirality : 0.040 0.189 5902 Planarity : 0.003 0.057 6382 Dihedral : 5.547 82.629 5708 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.12), residues: 5228 helix: 2.17 (0.09), residues: 3282 sheet: -0.85 (0.26), residues: 422 loop : -0.74 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 537 TYR 0.027 0.001 TYR E 256 PHE 0.023 0.002 PHE E 482 TRP 0.021 0.001 TRP E 694 HIS 0.008 0.001 HIS A2118 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (34935) covalent geometry : angle 0.50684 / 0.28 (47771) hydrogen bonds : bond 0.03215 / 2.13 ( 2568) hydrogen bonds : angle 3.90856 / 2.74 ( 7386) metal coordination : bond 0.02737 / 1.37 ( 4) metal coordination : angle 14.67676 / 8.58 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8357 (m110) cc_final: 0.8149 (m-40) REVERT: A 70 LYS cc_start: 0.8927 (pttt) cc_final: 0.8607 (pttp) REVERT: A 466 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 715 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6679 (mm-30) REVERT: A 782 MET cc_start: 0.8090 (tpp) cc_final: 0.7793 (tpt) REVERT: A 992 MET cc_start: 0.7103 (ttm) cc_final: 0.6774 (ttm) REVERT: A 1210 MET cc_start: 0.8952 (mmp) cc_final: 0.8685 (mmm) REVERT: A 1227 ASN cc_start: 0.7540 (p0) cc_final: 0.6547 (p0) REVERT: A 1340 GLU cc_start: 0.5284 (tp30) cc_final: 0.5070 (tp30) REVERT: A 1956 LEU cc_start: 0.8355 (tp) cc_final: 0.8012 (tp) REVERT: E 93 GLN cc_start: 0.8474 (tp40) cc_final: 0.8186 (tp40) REVERT: E 166 PHE cc_start: 0.7931 (t80) cc_final: 0.7717 (t80) REVERT: E 185 MET cc_start: 0.7759 (tpp) cc_final: 0.7383 (tpt) REVERT: E 215 ASN cc_start: 0.7746 (p0) cc_final: 0.7154 (t0) REVERT: E 226 TYR cc_start: 0.6537 (p90) cc_final: 0.6306 (p90) REVERT: E 234 LEU cc_start: 0.8208 (mp) cc_final: 0.7982 (tt) REVERT: E 414 MET cc_start: 0.7049 (ppp) cc_final: 0.6673 (ppp) REVERT: E 441 ASP cc_start: 0.6834 (m-30) cc_final: 0.6596 (m-30) REVERT: E 835 MET cc_start: 0.7978 (mmm) cc_final: 0.7751 (mmm) REVERT: E 967 MET cc_start: 0.6757 (mtp) cc_final: 0.6406 (tpp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2043 time to fit residues: 111.4834 Evaluate side-chains 277 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 317 optimal weight: 9.9990 chunk 283 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 311 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 477 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 511 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1067 HIS ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.096350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084588 restraints weight = 154946.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.084040 restraints weight = 181545.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084500 restraints weight = 157848.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.084395 restraints weight = 100927.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.084651 restraints weight = 94196.004| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34939 Z= 0.157 Angle : 0.517 18.468 47773 Z= 0.276 Chirality : 0.040 0.175 5902 Planarity : 0.003 0.058 6382 Dihedral : 5.436 84.185 5708 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.12), residues: 5228 helix: 2.27 (0.09), residues: 3276 sheet: -0.82 (0.27), residues: 418 loop : -0.65 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 537 TYR 0.025 0.001 TYR E 256 PHE 0.024 0.002 PHE A1296 TRP 0.018 0.001 TRP E 694 HIS 0.008 0.001 HIS A2118 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (34935) covalent geometry : angle 0.50948 / 0.28 (47771) hydrogen bonds : bond 0.03165 / 2.10 ( 2568) hydrogen bonds : angle 3.83177 / 2.69 ( 7386) metal coordination : bond 0.02417 / 1.21 ( 4) metal coordination : angle 13.57176 / 7.92 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8919 (pttt) cc_final: 0.8630 (pttp) REVERT: A 450 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7813 (mtmm) REVERT: A 466 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 715 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6672 (mm-30) REVERT: A 782 MET cc_start: 0.8031 (tpp) cc_final: 0.7758 (tpt) REVERT: A 992 MET cc_start: 0.6997 (ttm) cc_final: 0.6768 (ttm) REVERT: A 1104 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6945 (tp-100) REVERT: A 1210 MET cc_start: 0.9004 (mmp) cc_final: 0.8723 (mmm) REVERT: A 1227 ASN cc_start: 0.7547 (p0) cc_final: 0.7084 (p0) REVERT: A 1340 GLU cc_start: 0.5241 (tp30) cc_final: 0.5001 (tp30) REVERT: A 1956 LEU cc_start: 0.8290 (tp) cc_final: 0.7987 (tp) REVERT: E 93 GLN cc_start: 0.8427 (tp40) cc_final: 0.8127 (tp40) REVERT: E 166 PHE cc_start: 0.7904 (t80) cc_final: 0.7695 (t80) REVERT: E 185 MET cc_start: 0.7742 (tpp) cc_final: 0.7401 (tpt) REVERT: E 215 ASN cc_start: 0.7731 (p0) cc_final: 0.7153 (t0) REVERT: E 234 LEU cc_start: 0.8232 (mp) cc_final: 0.8000 (tt) REVERT: E 255 GLU cc_start: 0.8052 (tt0) cc_final: 0.7831 (tt0) REVERT: E 414 MET cc_start: 0.7054 (ppp) cc_final: 0.6678 (ppp) REVERT: E 441 ASP cc_start: 0.6809 (m-30) cc_final: 0.6577 (m-30) REVERT: E 535 MET cc_start: 0.8197 (tmm) cc_final: 0.7851 (ttt) REVERT: E 827 MET cc_start: 0.3393 (mtm) cc_final: 0.3097 (mtt) REVERT: E 967 MET cc_start: 0.6657 (mtp) cc_final: 0.6286 (mmm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2074 time to fit residues: 111.7427 Evaluate side-chains 287 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 367 optimal weight: 40.0000 chunk 229 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 63 optimal weight: 0.0050 chunk 338 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 374 optimal weight: 30.0000 chunk 339 optimal weight: 8.9990 chunk 53 optimal weight: 0.1980 chunk 153 optimal weight: 0.4980 chunk 311 optimal weight: 20.0000 overall best weight: 3.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 711 HIS A1249 ASN ** A1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.094951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083348 restraints weight = 155852.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.082664 restraints weight = 189983.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083272 restraints weight = 162869.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083144 restraints weight = 106365.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083364 restraints weight = 99793.760| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 34939 Z= 0.290 Angle : 0.641 25.244 47773 Z= 0.339 Chirality : 0.044 0.221 5902 Planarity : 0.004 0.058 6382 Dihedral : 5.842 83.639 5708 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.09 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.12), residues: 5228 helix: 1.98 (0.09), residues: 3272 sheet: -0.85 (0.27), residues: 406 loop : -0.79 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 561 TYR 0.025 0.002 TYR E 229 PHE 0.048 0.002 PHE A 526 TRP 0.025 0.002 TRP E 694 HIS 0.012 0.002 HIS A2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.29 (34935) covalent geometry : angle 0.62991 / 0.34 (47771) hydrogen bonds : bond 0.03895 / 2.59 ( 2568) hydrogen bonds : angle 4.25236 / 2.99 ( 7386) metal coordination : bond 0.04227 / 2.11 ( 4) metal coordination : angle 18.39816 / 10.76 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10456 Ramachandran restraints generated. 5228 Oldfield, 0 Emsley, 5228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8952 (pttt) cc_final: 0.8640 (pttp) REVERT: A 466 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 489 ASN cc_start: 0.8056 (t0) cc_final: 0.7554 (t0) REVERT: A 567 TYR cc_start: 0.7807 (t80) cc_final: 0.7449 (t80) REVERT: A 604 LYS cc_start: 0.8283 (tmtt) cc_final: 0.8057 (tptp) REVERT: A 715 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6641 (mm-30) REVERT: A 782 MET cc_start: 0.7934 (tpp) cc_final: 0.7657 (tpt) REVERT: A 1104 GLN cc_start: 0.7405 (tp-100) cc_final: 0.7055 (tp-100) REVERT: A 1210 MET cc_start: 0.9020 (mmp) cc_final: 0.8763 (mmm) REVERT: A 1227 ASN cc_start: 0.7488 (p0) cc_final: 0.6547 (p0) REVERT: E 185 MET cc_start: 0.7776 (tpp) cc_final: 0.7443 (tpt) REVERT: E 215 ASN cc_start: 0.7722 (p0) cc_final: 0.7150 (t0) REVERT: E 234 LEU cc_start: 0.8278 (mp) cc_final: 0.7966 (tt) REVERT: E 255 GLU cc_start: 0.8051 (tt0) cc_final: 0.7827 (tt0) REVERT: E 441 ASP cc_start: 0.6898 (m-30) cc_final: 0.6630 (m-30) REVERT: E 967 MET cc_start: 0.6769 (mtp) cc_final: 0.6372 (mmm) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1955 time to fit residues: 106.4117 Evaluate side-chains 285 residues out of total 4841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 86 optimal weight: 0.7980 chunk 279 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 369 optimal weight: 8.9990 chunk 529 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 chunk 364 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 577 ASN A1249 ASN A1257 HIS ** A2079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.095799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084000 restraints weight = 145527.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.083133 restraints weight = 160050.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.083731 restraints weight = 142490.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083835 restraints weight = 92046.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.084045 restraints weight = 82758.152| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34939 Z= 0.120 Angle : 0.495 17.725 47773 Z= 0.265 Chirality : 0.039 0.173 5902 Planarity : 0.003 0.086 6382 Dihedral : 5.407 85.212 5708 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.81 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.12), residues: 5228 helix: 2.31 (0.09), residues: 3281 sheet: -0.75 (0.27), residues: 404 loop : -0.64 (0.17), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1941 TYR 0.022 0.001 TYR E 229 PHE 0.027 0.001 PHE A1094 TRP 0.017 0.001 TRP A2590 HIS 0.007 0.001 HIS A2118 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (34935) covalent geometry : angle 0.48724 / 0.26 (47771) hydrogen bonds : bond 0.02947 / 1.95 ( 2568) hydrogen bonds : angle 3.72972 / 2.62 ( 7386) metal coordination : bond 0.02449 / 1.22 ( 4) metal coordination : angle 13.24719 / 7.71 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.21 seconds wall clock time: 98 minutes 14.74 seconds (5894.74 seconds total)