Starting phenix.real_space_refine on Tue Dec 31 07:17:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.map" model { file = "/net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eeb_28050/12_2024/8eeb_28050.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9410 2.51 5 N 2567 2.21 5 O 2629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14672 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 14454 Classifications: {'peptide': 1873} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 117, 'TRANS': 1755} Chain breaks: 7 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.06, per 1000 atoms: 0.62 Number of scatterers: 14672 At special positions: 0 Unit cell: (107.569, 111.125, 212.471, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2629 8.00 N 2567 7.00 C 9410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A1345 " - pdb=" SG CYS A1359 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A2201 " - " ASN A 78 " " NAG A2202 " - " ASN A 98 " " NAG A2203 " - " ASN A 340 " " NAG A2204 " - " ASN A1335 " " NAG B 1 " - " ASN A 312 " " NAG C 1 " - " ASN A1381 " " NAG D 1 " - " ASN A1386 " " NAG E 1 " - " ASN A1457 " " NAG F 1 " - " ASN A1518 " Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.0 seconds 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 11 sheets defined 59.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.571A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 46 Proline residue: A 32 - end of helix removed outlier: 3.900A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.596A pdb=" N GLU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.234A pdb=" N GLY A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 135 Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 197 through 208 removed outlier: 3.815A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.655A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.626A pdb=" N HIS A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.885A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.560A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.691A pdb=" N ALA A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 385 through 406 removed outlier: 4.523A pdb=" N CYS A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.589A pdb=" N SER A 446 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 541 through 575 removed outlier: 3.854A pdb=" N VAL A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Proline residue: A 551 - end of helix removed outlier: 5.039A pdb=" N TYR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 600 through 617 removed outlier: 3.739A pdb=" N LEU A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 647 removed outlier: 4.031A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 4.318A pdb=" N GLY A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.703A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 removed outlier: 3.766A pdb=" N ARG A 686 " --> pdb=" O PRO A 682 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 709 Processing helix chain 'A' and resid 715 through 719 removed outlier: 4.015A pdb=" N VAL A 719 " --> pdb=" O TRP A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 877 through 881 Proline residue: A 881 - end of helix Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.626A pdb=" N GLY A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 927 removed outlier: 3.567A pdb=" N GLU A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.150A pdb=" N SER A 934 " --> pdb=" O VAL A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 953 removed outlier: 3.890A pdb=" N LEU A 948 " --> pdb=" O MET A 944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 985 removed outlier: 4.132A pdb=" N ARG A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 4.375A pdb=" N LEU A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A1004 " --> pdb=" O GLU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1086 Processing helix chain 'A' and resid 1109 through 1122 removed outlier: 3.694A pdb=" N PHE A1113 " --> pdb=" O HIS A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1150 removed outlier: 3.986A pdb=" N ILE A1142 " --> pdb=" O SER A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1235 removed outlier: 4.121A pdb=" N SER A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1256 removed outlier: 3.776A pdb=" N LEU A1245 " --> pdb=" O ALA A1241 " (cutoff:3.500A) Proline residue: A1246 - end of helix removed outlier: 3.772A pdb=" N VAL A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A1255 " --> pdb=" O GLY A1251 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1290 through 1305 removed outlier: 3.538A pdb=" N GLY A1305 " --> pdb=" O LEU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1315 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1388 through 1400 Proline residue: A1396 - end of helix removed outlier: 3.635A pdb=" N VAL A1399 " --> pdb=" O TYR A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1404 removed outlier: 4.209A pdb=" N LYS A1404 " --> pdb=" O GLN A1401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1428 through 1443 removed outlier: 3.658A pdb=" N LEU A1432 " --> pdb=" O SER A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1464 Processing helix chain 'A' and resid 1465 through 1467 No H-bonds generated for 'chain 'A' and resid 1465 through 1467' Processing helix chain 'A' and resid 1481 through 1499 removed outlier: 3.521A pdb=" N ALA A1485 " --> pdb=" O HIS A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1508 removed outlier: 4.188A pdb=" N HIS A1506 " --> pdb=" O GLY A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1530 removed outlier: 4.020A pdb=" N LEU A1529 " --> pdb=" O SER A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1553 removed outlier: 3.796A pdb=" N PHE A1548 " --> pdb=" O PHE A1544 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Proline residue: A1550 - end of helix removed outlier: 3.837A pdb=" N PHE A1553 " --> pdb=" O VAL A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1563 removed outlier: 3.978A pdb=" N LEU A1557 " --> pdb=" O PHE A1553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1563 " --> pdb=" O GLU A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1564 through 1571 Processing helix chain 'A' and resid 1575 through 1606 removed outlier: 4.314A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix Processing helix chain 'A' and resid 1607 through 1611 Processing helix chain 'A' and resid 1615 through 1631 Processing helix chain 'A' and resid 1632 through 1639 Proline residue: A1636 - end of helix removed outlier: 3.668A pdb=" N PHE A1639 " --> pdb=" O PRO A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1671 Processing helix chain 'A' and resid 1675 through 1686 removed outlier: 3.723A pdb=" N GLU A1679 " --> pdb=" O GLN A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1716 removed outlier: 3.566A pdb=" N ARG A1715 " --> pdb=" O ASP A1711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1716 " --> pdb=" O ALA A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1753 Proline residue: A1742 - end of helix removed outlier: 3.919A pdb=" N LEU A1745 " --> pdb=" O GLY A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1786 Processing helix chain 'A' and resid 1832 through 1842 Processing helix chain 'A' and resid 1861 through 1868 removed outlier: 4.206A pdb=" N SER A1868 " --> pdb=" O ALA A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1895 Processing helix chain 'A' and resid 1898 through 1912 removed outlier: 4.209A pdb=" N ALA A1903 " --> pdb=" O GLU A1899 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A1904 " --> pdb=" O ALA A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1941 removed outlier: 3.539A pdb=" N LYS A1931 " --> pdb=" O SER A1927 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A1932 " --> pdb=" O GLY A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1975 removed outlier: 3.523A pdb=" N GLY A1975 " --> pdb=" O VAL A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1992 Processing helix chain 'A' and resid 2008 through 2016 Processing helix chain 'A' and resid 2030 through 2042 removed outlier: 4.370A pdb=" N ALA A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A2037 " --> pdb=" O PRO A2033 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A2042 " --> pdb=" O VAL A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2081 removed outlier: 3.503A pdb=" N GLY A2072 " --> pdb=" O ALA A2068 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU A2073 " --> pdb=" O ARG A2069 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA A2079 " --> pdb=" O ALA A2075 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A2080 " --> pdb=" O VAL A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2103 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.586A pdb=" N VAL A1280 " --> pdb=" O GLY A1415 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N PHE A1417 " --> pdb=" O VAL A1280 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N PHE A1282 " --> pdb=" O PHE A1417 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU A1419 " --> pdb=" O PHE A1282 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N SER A1284 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1283 " --> pdb=" O GLN A1380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 297 removed outlier: 6.028A pdb=" N LEU A 296 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 462 " --> pdb=" O THR A1511 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A1513 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE A 464 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 807 through 808 removed outlier: 3.811A pdb=" N VAL A 807 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 813 removed outlier: 4.610A pdb=" N LEU A 812 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 862 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 883 through 886 removed outlier: 6.489A pdb=" N GLY A 884 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP A 964 " --> pdb=" O GLY A 884 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS A 886 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 837 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 993 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A1007 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A1008 " --> pdb=" O CYS A1019 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS A1019 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A1010 " --> pdb=" O CYS A1017 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 866 through 867 Processing sheet with id=AA8, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.598A pdb=" N VAL A1092 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1100 " --> pdb=" O VAL A1092 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1810 through 1817 removed outlier: 4.934A pdb=" N ASP A1811 " --> pdb=" O LYS A1800 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A1800 " --> pdb=" O ASP A1811 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU A1815 " --> pdb=" O ARG A1796 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG A1796 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A1817 " --> pdb=" O VAL A1794 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A1794 " --> pdb=" O ILE A1817 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1869 through 1872 removed outlier: 6.611A pdb=" N PHE A1823 " --> pdb=" O LEU A1980 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A1994 " --> pdb=" O CYS A1822 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2046 through 2048 removed outlier: 3.993A pdb=" N GLU A2046 " --> pdb=" O GLN A2058 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A2085 " --> pdb=" O ARG A2025 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 4.72 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: 4781 1.34 - 1.46: 2934 1.46 - 1.58: 7205 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 15020 Sorted by residual: bond pdb=" C1 NAG A2202 " pdb=" O5 NAG A2202 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 NAG A2203 " pdb=" O5 NAG A2203 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 ... (remaining 15015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20015 2.04 - 4.09: 326 4.09 - 6.13: 68 6.13 - 8.17: 18 8.17 - 10.22: 1 Bond angle restraints: 20428 Sorted by residual: angle pdb=" C LEU A1689 " pdb=" CA LEU A1689 " pdb=" CB LEU A1689 " ideal model delta sigma weight residual 117.23 109.53 7.70 1.36e+00 5.41e-01 3.21e+01 angle pdb=" CA LEU A1689 " pdb=" C LEU A1689 " pdb=" N ILE A1690 " ideal model delta sigma weight residual 119.98 116.09 3.89 8.50e-01 1.38e+00 2.09e+01 angle pdb=" N GLN A 349 " pdb=" CA GLN A 349 " pdb=" CB GLN A 349 " ideal model delta sigma weight residual 110.16 115.58 -5.42 1.48e+00 4.57e-01 1.34e+01 angle pdb=" C VAL A 311 " pdb=" N ASN A 312 " pdb=" CA ASN A 312 " ideal model delta sigma weight residual 122.56 116.67 5.89 1.72e+00 3.38e-01 1.17e+01 angle pdb=" N LEU A1387 " pdb=" CA LEU A1387 " pdb=" C LEU A1387 " ideal model delta sigma weight residual 113.72 108.76 4.96 1.52e+00 4.33e-01 1.06e+01 ... (remaining 20423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 8471 22.19 - 44.38: 587 44.38 - 66.57: 57 66.57 - 88.76: 25 88.76 - 110.95: 12 Dihedral angle restraints: 9152 sinusoidal: 3819 harmonic: 5333 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual 93.00 156.53 -63.53 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CA ARG A1385 " pdb=" C ARG A1385 " pdb=" N ASN A1386 " pdb=" CA ASN A1386 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N SER A 342 " pdb=" CA SER A 342 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 9149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 2359 0.186 - 0.371: 7 0.371 - 0.557: 0 0.557 - 0.743: 0 0.743 - 0.928: 1 Chirality restraints: 2367 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1386 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" C1 NAG A2204 " pdb=" ND2 ASN A1335 " pdb=" C2 NAG A2204 " pdb=" O5 NAG A2204 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2364 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1386 " 0.043 2.00e-02 2.50e+03 4.09e-02 2.09e+01 pdb=" CG ASN A1386 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A1386 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A1386 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 312 " 0.038 2.00e-02 2.50e+03 3.57e-02 1.60e+01 pdb=" CG ASN A 312 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 312 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 312 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1381 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.25e+00 pdb=" CG ASN A1381 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1381 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A1381 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.019 2.00e-02 2.50e+03 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2094 2.76 - 3.29: 14788 3.29 - 3.83: 24297 3.83 - 4.36: 25856 4.36 - 4.90: 45066 Nonbonded interactions: 112101 Sorted by model distance: nonbonded pdb=" OE2 GLU A 28 " pdb=" OG SER A 561 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP A1389 " pdb=" O6 NAG D 1 " model vdw 2.253 3.040 nonbonded pdb=" O GLY A1832 " pdb=" OG SER A1835 " model vdw 2.255 3.040 nonbonded pdb=" O ALA A 372 " pdb=" OG SER A 375 " model vdw 2.267 3.040 nonbonded pdb=" O LEU A 290 " pdb=" NZ LYS A 411 " model vdw 2.280 3.120 ... (remaining 112096 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 'B' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.250 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.003 0.074 15020 Z= 0.190 Angle : 0.656 10.217 20428 Z= 0.314 Chirality : 0.046 0.928 2367 Planarity : 0.004 0.046 2607 Dihedral : 15.264 110.953 5710 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1857 helix: 1.63 (0.17), residues: 965 sheet: -0.10 (0.43), residues: 147 loop : -1.40 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1965 HIS 0.005 0.001 HIS A1693 PHE 0.030 0.001 PHE A1283 TYR 0.013 0.001 TYR A 384 ARG 0.004 0.000 ARG A1453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.588 Fit side-chains REVERT: A 16 MET cc_start: 0.8589 (mmt) cc_final: 0.8071 (mmt) REVERT: A 1568 LEU cc_start: 0.9549 (tt) cc_final: 0.9122 (mp) REVERT: A 1703 MET cc_start: 0.7873 (mmp) cc_final: 0.7310 (tpp) REVERT: A 2006 LEU cc_start: 0.8030 (tp) cc_final: 0.7730 (tp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2344 time to fit residues: 38.3555 Evaluate side-chains 71 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 9.9990 chunk 141 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 109 optimal weight: 0.0970 chunk 169 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15020 Z= 0.151 Angle : 0.632 11.349 20428 Z= 0.292 Chirality : 0.041 0.302 2367 Planarity : 0.004 0.044 2607 Dihedral : 9.054 95.870 2369 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.52 % Allowed : 6.27 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1857 helix: 1.75 (0.17), residues: 985 sheet: -0.06 (0.42), residues: 146 loop : -1.49 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1965 HIS 0.005 0.001 HIS A1693 PHE 0.025 0.001 PHE A1544 TYR 0.019 0.001 TYR A1871 ARG 0.011 0.000 ARG A2025 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.8635 (mmt) cc_final: 0.8134 (mmt) REVERT: A 407 LEU cc_start: 0.8703 (tp) cc_final: 0.8487 (tt) REVERT: A 839 PHE cc_start: 0.8436 (t80) cc_final: 0.8179 (t80) REVERT: A 1358 ASP cc_start: 0.8243 (t0) cc_final: 0.7625 (t0) REVERT: A 1703 MET cc_start: 0.7901 (mmp) cc_final: 0.7297 (tpp) REVERT: A 1807 MET cc_start: 0.2666 (ttt) cc_final: 0.2464 (ttt) REVERT: A 2006 LEU cc_start: 0.8076 (tp) cc_final: 0.7705 (tp) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 0.2563 time to fit residues: 41.0567 Evaluate side-chains 85 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1667 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15020 Z= 0.277 Angle : 0.658 10.031 20428 Z= 0.310 Chirality : 0.042 0.321 2367 Planarity : 0.004 0.043 2607 Dihedral : 8.024 94.853 2369 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.85 % Allowed : 10.78 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1857 helix: 1.65 (0.17), residues: 998 sheet: -0.32 (0.41), residues: 158 loop : -1.56 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1965 HIS 0.005 0.001 HIS A1866 PHE 0.017 0.002 PHE A1694 TYR 0.016 0.002 TYR A1579 ARG 0.006 0.000 ARG A1973 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.774 Fit side-chains REVERT: A 839 PHE cc_start: 0.8373 (t80) cc_final: 0.8109 (t80) REVERT: A 1568 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9102 (mp) REVERT: A 1703 MET cc_start: 0.8088 (mmp) cc_final: 0.7423 (tpp) REVERT: A 1807 MET cc_start: 0.2770 (ttt) cc_final: 0.2559 (ttt) REVERT: A 2006 LEU cc_start: 0.8111 (tp) cc_final: 0.7675 (tp) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.2629 time to fit residues: 42.5929 Evaluate side-chains 86 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1542 VAL Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1577 THR Chi-restraints excluded: chain A residue 1794 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A1706 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15020 Z= 0.150 Angle : 0.613 10.972 20428 Z= 0.282 Chirality : 0.040 0.302 2367 Planarity : 0.004 0.044 2607 Dihedral : 7.375 89.508 2369 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.65 % Allowed : 13.13 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1857 helix: 1.82 (0.17), residues: 990 sheet: -0.34 (0.41), residues: 165 loop : -1.52 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1965 HIS 0.005 0.001 HIS A1693 PHE 0.016 0.001 PHE A1667 TYR 0.022 0.001 TYR A1871 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 839 PHE cc_start: 0.8330 (t80) cc_final: 0.8058 (t80) REVERT: A 1568 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 1703 MET cc_start: 0.7884 (mmp) cc_final: 0.7345 (tpp) REVERT: A 1807 MET cc_start: 0.2764 (ttt) cc_final: 0.2556 (ttt) REVERT: A 2006 LEU cc_start: 0.8117 (tp) cc_final: 0.7650 (tp) outliers start: 10 outliers final: 2 residues processed: 93 average time/residue: 0.2330 time to fit residues: 36.3513 Evaluate side-chains 84 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15020 Z= 0.200 Angle : 0.626 13.019 20428 Z= 0.289 Chirality : 0.040 0.309 2367 Planarity : 0.004 0.043 2607 Dihedral : 7.235 88.914 2369 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 14.83 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1857 helix: 1.81 (0.17), residues: 992 sheet: -0.29 (0.41), residues: 157 loop : -1.57 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1965 HIS 0.005 0.001 HIS A1693 PHE 0.017 0.001 PHE A1667 TYR 0.015 0.001 TYR A1871 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.540 Fit side-chains REVERT: A 839 PHE cc_start: 0.8348 (t80) cc_final: 0.8094 (t80) REVERT: A 1568 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 1703 MET cc_start: 0.7925 (mmp) cc_final: 0.7286 (tpp) REVERT: A 1807 MET cc_start: 0.2787 (ttt) cc_final: 0.2584 (ttt) REVERT: A 2006 LEU cc_start: 0.8129 (tp) cc_final: 0.7628 (tp) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.2245 time to fit residues: 36.0955 Evaluate side-chains 91 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1542 VAL Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1577 THR Chi-restraints excluded: chain A residue 1794 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 0.0170 chunk 44 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15020 Z= 0.157 Angle : 0.618 14.291 20428 Z= 0.281 Chirality : 0.040 0.301 2367 Planarity : 0.004 0.044 2607 Dihedral : 7.033 85.688 2369 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.11 % Allowed : 15.81 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1857 helix: 1.87 (0.17), residues: 992 sheet: -0.31 (0.41), residues: 163 loop : -1.53 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1965 HIS 0.006 0.001 HIS A1693 PHE 0.017 0.001 PHE A1667 TYR 0.015 0.001 TYR A1871 ARG 0.003 0.000 ARG A1608 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.674 Fit side-chains revert: symmetry clash REVERT: A 839 PHE cc_start: 0.8329 (t80) cc_final: 0.8074 (t80) REVERT: A 1703 MET cc_start: 0.7933 (mmp) cc_final: 0.7302 (tpp) REVERT: A 1807 MET cc_start: 0.2823 (ttt) cc_final: 0.2620 (ttt) REVERT: A 1869 MET cc_start: 0.7278 (ttt) cc_final: 0.6851 (tpt) REVERT: A 1948 PHE cc_start: 0.8304 (m-10) cc_final: 0.8096 (m-10) REVERT: A 2006 LEU cc_start: 0.8133 (tp) cc_final: 0.7605 (tp) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.2408 time to fit residues: 42.5376 Evaluate side-chains 102 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1693 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15020 Z= 0.264 Angle : 0.668 16.853 20428 Z= 0.310 Chirality : 0.041 0.313 2367 Planarity : 0.004 0.043 2607 Dihedral : 7.143 86.266 2369 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.37 % Allowed : 16.26 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1857 helix: 1.70 (0.17), residues: 998 sheet: -0.35 (0.42), residues: 157 loop : -1.60 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1965 HIS 0.016 0.001 HIS A1693 PHE 0.020 0.001 PHE A1667 TYR 0.012 0.001 TYR A1871 ARG 0.009 0.000 ARG A1973 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 839 PHE cc_start: 0.8307 (t80) cc_final: 0.8004 (t80) REVERT: A 1282 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: A 1703 MET cc_start: 0.8121 (mmp) cc_final: 0.7393 (tpp) REVERT: A 1807 MET cc_start: 0.2779 (ttt) cc_final: 0.2563 (ttt) REVERT: A 1869 MET cc_start: 0.7501 (ttt) cc_final: 0.7018 (tpt) REVERT: A 2006 LEU cc_start: 0.8148 (tp) cc_final: 0.7807 (tp) outliers start: 21 outliers final: 14 residues processed: 104 average time/residue: 0.2316 time to fit residues: 39.6261 Evaluate side-chains 98 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1282 PHE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1577 THR Chi-restraints excluded: chain A residue 1646 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A1693 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15020 Z= 0.259 Angle : 0.683 18.712 20428 Z= 0.315 Chirality : 0.042 0.318 2367 Planarity : 0.004 0.043 2607 Dihedral : 7.110 83.592 2369 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.24 % Allowed : 16.66 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1857 helix: 1.63 (0.17), residues: 997 sheet: -0.48 (0.41), residues: 158 loop : -1.64 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1965 HIS 0.004 0.001 HIS A1693 PHE 0.015 0.001 PHE A1667 TYR 0.015 0.001 TYR A1579 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 839 PHE cc_start: 0.8289 (t80) cc_final: 0.7992 (t80) REVERT: A 1282 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: A 1703 MET cc_start: 0.8131 (mmp) cc_final: 0.7350 (tpp) REVERT: A 1869 MET cc_start: 0.7471 (ttt) cc_final: 0.6972 (tpt) REVERT: A 1948 PHE cc_start: 0.8209 (m-10) cc_final: 0.8006 (m-10) REVERT: A 2006 LEU cc_start: 0.8185 (tp) cc_final: 0.7608 (tp) outliers start: 19 outliers final: 15 residues processed: 102 average time/residue: 0.2294 time to fit residues: 39.4813 Evaluate side-chains 99 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1282 PHE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1693 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 157 optimal weight: 0.2980 chunk 167 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15020 Z= 0.191 Angle : 0.685 19.988 20428 Z= 0.311 Chirality : 0.041 0.311 2367 Planarity : 0.004 0.044 2607 Dihedral : 7.006 82.055 2369 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.11 % Allowed : 17.24 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1857 helix: 1.68 (0.17), residues: 996 sheet: -0.41 (0.41), residues: 157 loop : -1.64 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A1965 HIS 0.011 0.001 HIS A1693 PHE 0.020 0.001 PHE A1691 TYR 0.015 0.001 TYR A1579 ARG 0.002 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 839 PHE cc_start: 0.8287 (t80) cc_final: 0.7986 (t80) REVERT: A 1282 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: A 1703 MET cc_start: 0.8132 (mmp) cc_final: 0.7450 (tpp) REVERT: A 1869 MET cc_start: 0.7413 (ttt) cc_final: 0.6904 (tpt) REVERT: A 2006 LEU cc_start: 0.8189 (tp) cc_final: 0.7623 (tp) outliers start: 17 outliers final: 16 residues processed: 96 average time/residue: 0.2246 time to fit residues: 35.8872 Evaluate side-chains 99 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1282 PHE Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1577 THR Chi-restraints excluded: chain A residue 1646 THR Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1794 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.0370 chunk 117 optimal weight: 3.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15020 Z= 0.156 Angle : 0.673 16.829 20428 Z= 0.302 Chirality : 0.041 0.302 2367 Planarity : 0.004 0.044 2607 Dihedral : 6.857 79.944 2369 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.78 % Allowed : 17.64 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1857 helix: 1.76 (0.17), residues: 995 sheet: -0.35 (0.41), residues: 156 loop : -1.60 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A1965 HIS 0.017 0.001 HIS A1693 PHE 0.022 0.001 PHE A1691 TYR 0.016 0.001 TYR A1579 ARG 0.003 0.000 ARG A 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3714 Ramachandran restraints generated. 1857 Oldfield, 0 Emsley, 1857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 347 MET cc_start: 0.9294 (mmm) cc_final: 0.8749 (mpp) REVERT: A 839 PHE cc_start: 0.8275 (t80) cc_final: 0.8022 (t80) REVERT: A 1625 LEU cc_start: 0.8317 (tp) cc_final: 0.8082 (tp) REVERT: A 1703 MET cc_start: 0.8155 (mmp) cc_final: 0.7350 (tpp) REVERT: A 1737 MET cc_start: 0.6245 (ppp) cc_final: 0.5582 (ppp) REVERT: A 1869 MET cc_start: 0.7355 (ttt) cc_final: 0.6835 (tpt) REVERT: A 2006 LEU cc_start: 0.8146 (tp) cc_final: 0.7563 (tp) outliers start: 12 outliers final: 12 residues processed: 98 average time/residue: 0.2206 time to fit residues: 36.5919 Evaluate side-chains 100 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1359 CYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1693 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.096568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065626 restraints weight = 62067.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066261 restraints weight = 37755.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066653 restraints weight = 24353.175| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15020 Z= 0.158 Angle : 0.673 20.427 20428 Z= 0.300 Chirality : 0.040 0.299 2367 Planarity : 0.004 0.044 2607 Dihedral : 6.770 78.914 2369 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.85 % Allowed : 17.50 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1857 helix: 1.82 (0.17), residues: 995 sheet: -0.31 (0.41), residues: 156 loop : -1.60 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A1965 HIS 0.006 0.001 HIS A1567 PHE 0.021 0.001 PHE A1691 TYR 0.015 0.001 TYR A1579 ARG 0.004 0.000 ARG A1848 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2705.58 seconds wall clock time: 50 minutes 31.70 seconds (3031.70 seconds total)