Starting phenix.real_space_refine on Fri May 16 12:24:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.map" model { file = "/net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1o_38841/05_2025/8y1o_38841.cif" } resolution = 3.92 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= 0.001 sd= 0.024 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 64 5.16 5 C 9155 2.51 5 N 2511 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14226 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1844, 14226 Classifications: {'peptide': 1844} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 113, 'TRANS': 1730} Chain breaks: 8 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 Time building chain proxies: 7.99, per 1000 atoms: 0.56 Number of scatterers: 14226 At special positions: 0 Unit cell: (84.53, 100.58, 215.07, 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 64 16.00 O 2496 8.00 N 2511 7.00 C 9155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.02 Simple disulfide: pdb=" SG CYS A1017 " - pdb=" SG CYS A1150 " distance=2.03 Simple disulfide: pdb=" SG CYS A1345 " - pdb=" SG CYS A1359 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3378 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 56.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.628A pdb=" N MET A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.972A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.849A pdb=" N GLY A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 117 through 135 removed outlier: 4.116A pdb=" N ALA A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 197 through 208 removed outlier: 4.306A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.943A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 removed outlier: 4.043A pdb=" N HIS A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 338 removed outlier: 3.992A pdb=" N ASP A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.060A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLN A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 386 through 404 Processing helix chain 'A' and resid 417 through 431 Processing helix chain 'A' and resid 503 through 520 removed outlier: 3.571A pdb=" N GLY A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.598A pdb=" N THR A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.559A pdb=" N THR A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 617 removed outlier: 4.227A pdb=" N GLY A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Proline residue: A 602 - end of helix removed outlier: 3.832A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 648 removed outlier: 3.951A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 4.369A pdb=" N GLY A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.704A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 692 through 710 removed outlier: 3.531A pdb=" N ALA A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 735 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 848 through 854 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 898 through 910 Processing helix chain 'A' and resid 916 through 927 removed outlier: 4.324A pdb=" N ARG A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 952 removed outlier: 4.027A pdb=" N LEU A 948 " --> pdb=" O MET A 944 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.890A pdb=" N ARG A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1086 removed outlier: 3.745A pdb=" N LEU A1078 " --> pdb=" O GLY A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1125 removed outlier: 3.890A pdb=" N GLU A1119 " --> pdb=" O THR A1115 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1148 removed outlier: 3.696A pdb=" N ILE A1142 " --> pdb=" O SER A1138 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1235 removed outlier: 3.924A pdb=" N ARG A1234 " --> pdb=" O LEU A1230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1257 Proline residue: A1246 - end of helix removed outlier: 3.877A pdb=" N GLY A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.632A pdb=" N MET A1275 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A1277 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1304 removed outlier: 3.536A pdb=" N ALA A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1315 Processing helix chain 'A' and resid 1324 through 1334 removed outlier: 3.985A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1400 Proline residue: A1396 - end of helix removed outlier: 3.597A pdb=" N VAL A1399 " --> pdb=" O TYR A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1443 Processing helix chain 'A' and resid 1449 through 1464 removed outlier: 3.818A pdb=" N VAL A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) 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 1498 Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 4.050A pdb=" N SER A1525 " --> pdb=" O LYS A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1547 removed outlier: 3.994A pdb=" N VAL A1543 " --> pdb=" O SER A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1563 Processing helix chain 'A' and resid 1564 through 1571 removed outlier: 3.550A pdb=" N LEU A1568 " --> pdb=" O ARG A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1605 removed outlier: 4.368A pdb=" N LEU A1585 " --> pdb=" O LEU A1581 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP A1586 " --> pdb=" O GLY A1582 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix removed outlier: 3.813A pdb=" N ILE A1597 " --> pdb=" O VAL A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1631 removed outlier: 3.785A pdb=" N THR A1631 " --> pdb=" O GLY A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 4.289A pdb=" N TYR A1635 " --> pdb=" O PRO A1632 " (cutoff:3.500A) Proline residue: A1636 - end of helix removed outlier: 3.748A pdb=" N PHE A1639 " --> pdb=" O PRO A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1671 removed outlier: 4.484A pdb=" N THR A1666 " --> pdb=" O GLY A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.527A pdb=" N GLU A1679 " --> pdb=" O GLN A1675 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A1689 " --> pdb=" O LYS A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1714 Processing helix chain 'A' and resid 1730 through 1753 removed outlier: 3.526A pdb=" N LEU A1734 " --> pdb=" O VAL A1730 " (cutoff:3.500A) Proline residue: A1742 - end of helix removed outlier: 3.830A pdb=" N THR A1748 " --> pdb=" O PHE A1744 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A1749 " --> pdb=" O LEU A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1786 removed outlier: 4.002A pdb=" N ARG A1782 " --> pdb=" O ARG A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1842 removed outlier: 3.770A pdb=" N VAL A1840 " --> pdb=" O THR A1836 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1866 Processing helix chain 'A' and resid 1883 through 1895 Processing helix chain 'A' and resid 1898 through 1912 removed outlier: 4.516A pdb=" N ALA A1903 " --> pdb=" O GLU A1899 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A1904 " --> pdb=" O ALA A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 removed outlier: 3.734A pdb=" N TYR A1926 " --> pdb=" O ALA A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1941 Processing helix chain 'A' and resid 1957 through 1974 Processing helix chain 'A' and resid 1985 through 1992 removed outlier: 3.861A pdb=" N GLU A1989 " --> pdb=" O MET A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2008 through 2017 Processing helix chain 'A' and resid 2030 through 2042 removed outlier: 4.181A pdb=" N ALA A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A2037 " --> pdb=" O PRO A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2078 removed outlier: 3.774A pdb=" N GLY A2072 " --> pdb=" O ALA A2068 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU A2073 " --> pdb=" O ARG A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2103 removed outlier: 3.884A pdb=" N LEU A2098 " --> pdb=" O GLU A2094 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.351A pdb=" N TYR A 528 " --> pdb=" O ILE A1473 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A1475 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN A 530 " --> pdb=" O PHE A1475 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A1418 " --> pdb=" O LYS A1472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 297 removed outlier: 5.867A pdb=" N LEU A 295 " --> pdb=" O GLU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 439 removed outlier: 6.776A pdb=" N VAL A 462 " --> pdb=" O THR A1511 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A1513 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 464 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 883 through 886 removed outlier: 6.815A pdb=" N GLY A 884 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 993 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 836 " --> pdb=" O ARG A1007 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA A1009 " --> pdb=" O ILE A 836 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 838 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL A1011 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 840 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A1018 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A1012 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1095 removed outlier: 6.802A pdb=" N VAL A1100 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU A1094 " --> pdb=" O GLU A1098 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1280 through 1282 removed outlier: 6.710A pdb=" N SER A1281 " --> pdb=" O GLN A1380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1815 through 1817 removed outlier: 3.627A pdb=" N LEU A1793 " --> pdb=" O ILE A1817 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1869 through 1870 removed outlier: 5.778A pdb=" N GLY A1870 " --> pdb=" O PHE A1948 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP A1950 " --> pdb=" O GLY A1870 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A1947 " --> pdb=" O MET A1979 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR A1981 " --> pdb=" O VAL A1947 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A1949 " --> pdb=" O THR A1981 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1823 " --> pdb=" O VAL A1978 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A1980 " --> pdb=" O PHE A1823 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY A1824 " --> pdb=" O ALA A1996 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N MET A1998 " --> pdb=" O GLY A1824 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A1826 " --> pdb=" O MET A1998 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2055 through 2058 removed outlier: 3.717A pdb=" N LEU A2055 " --> pdb=" O LEU A2024 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 2007 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: 5.65 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4672 1.35 - 1.47: 3547 1.47 - 1.60: 6251 1.60 - 1.73: 1 1.73 - 1.86: 96 Bond restraints: 14567 Sorted by residual: bond pdb=" N PRO A2060 " pdb=" CD PRO A2060 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.74e+01 bond pdb=" CA THR A1631 " pdb=" CB THR A1631 " ideal model delta sigma weight residual 1.531 1.585 -0.053 1.33e-02 5.65e+03 1.61e+01 bond pdb=" CB VAL A2038 " pdb=" CG1 VAL A2038 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.42e+01 bond pdb=" CB MET A1979 " pdb=" CG MET A1979 " ideal model delta sigma weight residual 1.520 1.632 -0.112 3.00e-02 1.11e+03 1.41e+01 bond pdb=" N PRO A1503 " pdb=" CD PRO A1503 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 14562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.69: 19683 5.69 - 11.38: 121 11.38 - 17.07: 7 17.07 - 22.76: 0 22.76 - 28.46: 1 Bond angle restraints: 19812 Sorted by residual: angle pdb=" CB MET A1979 " pdb=" CG MET A1979 " pdb=" SD MET A1979 " ideal model delta sigma weight residual 112.70 141.16 -28.46 3.00e+00 1.11e-01 9.00e+01 angle pdb=" N VAL A 898 " pdb=" CA VAL A 898 " pdb=" C VAL A 898 " ideal model delta sigma weight residual 111.00 120.27 -9.27 1.09e+00 8.42e-01 7.23e+01 angle pdb=" N LEU A 506 " pdb=" CA LEU A 506 " pdb=" C LEU A 506 " ideal model delta sigma weight residual 110.97 103.69 7.28 1.09e+00 8.42e-01 4.46e+01 angle pdb=" C THR A 897 " pdb=" CA THR A 897 " pdb=" CB THR A 897 " ideal model delta sigma weight residual 110.42 122.52 -12.10 1.99e+00 2.53e-01 3.70e+01 angle pdb=" N LEU A 70 " pdb=" CA LEU A 70 " pdb=" C LEU A 70 " ideal model delta sigma weight residual 110.97 104.47 6.50 1.09e+00 8.42e-01 3.55e+01 ... (remaining 19807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 7429 18.08 - 36.16: 935 36.16 - 54.24: 262 54.24 - 72.32: 31 72.32 - 90.40: 16 Dihedral angle restraints: 8673 sinusoidal: 3422 harmonic: 5251 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 -176.60 -90.40 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A1017 " pdb=" SG CYS A1017 " pdb=" SG CYS A1150 " pdb=" CB CYS A1150 " ideal model delta sinusoidal sigma weight residual -86.00 -157.24 71.24 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" C THR A 897 " pdb=" N THR A 897 " pdb=" CA THR A 897 " pdb=" CB THR A 897 " ideal model delta harmonic sigma weight residual -122.00 -137.54 15.54 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 8670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2175 0.118 - 0.237: 66 0.237 - 0.355: 12 0.355 - 0.473: 2 0.473 - 0.591: 3 Chirality restraints: 2258 Sorted by residual: chirality pdb=" CG LEU A1751 " pdb=" CB LEU A1751 " pdb=" CD1 LEU A1751 " pdb=" CD2 LEU A1751 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.74e+00 chirality pdb=" CA THR A 897 " pdb=" N THR A 897 " pdb=" C THR A 897 " pdb=" CB THR A 897 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CB VAL A 891 " pdb=" CA VAL A 891 " pdb=" CG1 VAL A 891 " pdb=" CG2 VAL A 891 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 2255 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 897 " 0.025 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" C THR A 897 " -0.090 2.00e-02 2.50e+03 pdb=" O THR A 897 " 0.035 2.00e-02 2.50e+03 pdb=" N VAL A 898 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2059 " -0.082 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A2060 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO A2060 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A2060 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 574 " -0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" CD GLU A 574 " 0.061 2.00e-02 2.50e+03 pdb=" OE1 GLU A 574 " -0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU A 574 " -0.022 2.00e-02 2.50e+03 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 19 2.32 - 2.97: 6264 2.97 - 3.61: 22215 3.61 - 4.26: 31787 4.26 - 4.90: 51921 Nonbonded interactions: 112206 Sorted by model distance: nonbonded pdb=" CD2 PHE A2042 " pdb=" CD1 LEU A2059 " model vdw 1.678 3.760 nonbonded pdb=" CG PHE A2042 " pdb=" CD1 LEU A2059 " model vdw 2.190 3.680 nonbonded pdb=" OG1 THR A2021 " pdb=" O SER A2089 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A1984 " pdb=" OE1 GLU A1986 " model vdw 2.236 3.040 nonbonded pdb=" O ARG A 334 " pdb=" OG1 THR A 337 " model vdw 2.247 3.040 ... (remaining 112201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.230 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.950 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.005 0.124 14572 Z= 0.251 Angle : 1.076 28.456 19822 Z= 0.542 Chirality : 0.059 0.591 2258 Planarity : 0.008 0.125 2544 Dihedral : 17.142 89.904 5280 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 29.90 % Favored : 70.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.18), residues: 1826 helix: -1.20 (0.16), residues: 940 sheet: -2.11 (0.35), residues: 199 loop : -2.29 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1965 HIS 0.012 0.001 HIS A1887 PHE 0.045 0.003 PHE A1963 TYR 0.041 0.002 TYR A1591 ARG 0.027 0.001 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.14434 ( 689) hydrogen bonds : angle 6.93585 ( 2007) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.77425 ( 10) covalent geometry : bond 0.00544 (14567) covalent geometry : angle 1.07641 (19812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1571 MET cc_start: 0.8070 (mmp) cc_final: 0.7851 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2227 time to fit residues: 53.8583 Evaluate side-chains 147 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.152156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121161 restraints weight = 37439.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.117605 restraints weight = 29142.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.118716 restraints weight = 23804.356| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14572 Z= 0.164 Angle : 0.674 11.822 19822 Z= 0.333 Chirality : 0.042 0.222 2258 Planarity : 0.005 0.072 2544 Dihedral : 5.128 26.777 2004 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.59 % Allowed : 26.45 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1826 helix: -0.38 (0.17), residues: 958 sheet: -1.98 (0.36), residues: 204 loop : -2.24 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1965 HIS 0.005 0.001 HIS A1887 PHE 0.028 0.002 PHE A1963 TYR 0.021 0.001 TYR A1591 ARG 0.006 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 689) hydrogen bonds : angle 5.21424 ( 2007) SS BOND : bond 0.00266 ( 5) SS BOND : angle 0.52945 ( 10) covalent geometry : bond 0.00361 (14567) covalent geometry : angle 0.67408 (19812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9136 (mmm) cc_final: 0.8851 (tpp) REVERT: A 967 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7557 (m) REVERT: A 998 LEU cc_start: 0.8823 (mt) cc_final: 0.8606 (mt) REVERT: A 1839 MET cc_start: 0.5708 (pmm) cc_final: 0.5507 (pmm) outliers start: 54 outliers final: 30 residues processed: 203 average time/residue: 0.2026 time to fit residues: 65.6843 Evaluate side-chains 176 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1634 MET Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 60 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 50.0000 chunk 22 optimal weight: 0.7980 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS ** A1752 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 = 0.4332 r_free = 0.4332 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106134 restraints weight = 37406.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106851 restraints weight = 26351.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106034 restraints weight = 20901.729| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14572 Z= 0.216 Angle : 0.710 11.162 19822 Z= 0.347 Chirality : 0.043 0.232 2258 Planarity : 0.005 0.063 2544 Dihedral : 5.098 28.237 2004 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.18 % Allowed : 26.71 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1826 helix: -0.09 (0.17), residues: 960 sheet: -2.13 (0.35), residues: 206 loop : -2.21 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1965 HIS 0.008 0.001 HIS A1887 PHE 0.047 0.002 PHE A1584 TYR 0.021 0.002 TYR A1591 ARG 0.005 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 689) hydrogen bonds : angle 5.06553 ( 2007) SS BOND : bond 0.00281 ( 5) SS BOND : angle 0.59957 ( 10) covalent geometry : bond 0.00486 (14567) covalent geometry : angle 0.71038 (19812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 162 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9263 (mmm) cc_final: 0.8894 (tpp) REVERT: A 192 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7724 (pp30) REVERT: A 308 MET cc_start: 0.8356 (mmp) cc_final: 0.8152 (mmp) REVERT: A 577 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8850 (pp) REVERT: A 870 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6529 (p-80) REVERT: A 967 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7827 (m) REVERT: A 1590 ASN cc_start: 0.8479 (t0) cc_final: 0.8196 (t0) REVERT: A 1703 MET cc_start: 0.8834 (ppp) cc_final: 0.8577 (ppp) REVERT: A 1868 SER cc_start: 0.3832 (OUTLIER) cc_final: 0.3586 (m) REVERT: A 1879 PHE cc_start: 0.8997 (m-80) cc_final: 0.8609 (m-10) REVERT: A 1979 MET cc_start: 0.7455 (mmm) cc_final: 0.6453 (mmm) outliers start: 78 outliers final: 42 residues processed: 223 average time/residue: 0.2017 time to fit residues: 72.4232 Evaluate side-chains 192 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1634 MET Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1868 SER Chi-restraints excluded: chain A residue 1881 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 183 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 0.0060 chunk 140 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1606 GLN ** A1752 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 = 0.4339 r_free = 0.4339 target = 0.149861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106221 restraints weight = 37429.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107391 restraints weight = 26064.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106426 restraints weight = 17448.565| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14572 Z= 0.188 Angle : 0.690 11.884 19822 Z= 0.334 Chirality : 0.043 0.240 2258 Planarity : 0.005 0.060 2544 Dihedral : 4.992 29.541 2004 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.72 % Allowed : 27.24 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1826 helix: 0.12 (0.17), residues: 956 sheet: -2.09 (0.36), residues: 206 loop : -2.15 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1965 HIS 0.011 0.001 HIS A1887 PHE 0.037 0.002 PHE A1605 TYR 0.019 0.001 TYR A1591 ARG 0.005 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 689) hydrogen bonds : angle 4.97284 ( 2007) SS BOND : bond 0.00238 ( 5) SS BOND : angle 0.66531 ( 10) covalent geometry : bond 0.00427 (14567) covalent geometry : angle 0.69006 (19812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9233 (mmm) cc_final: 0.8841 (tpp) REVERT: A 192 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7733 (pp30) REVERT: A 330 MET cc_start: 0.8776 (ppp) cc_final: 0.8543 (ppp) REVERT: A 577 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8879 (pp) REVERT: A 746 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7830 (tt) REVERT: A 870 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.6618 (p-80) REVERT: A 880 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7252 (mmm-85) REVERT: A 944 MET cc_start: 0.7982 (tmm) cc_final: 0.7735 (tmm) REVERT: A 967 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7843 (m) REVERT: A 971 ASP cc_start: 0.7832 (t0) cc_final: 0.7139 (p0) REVERT: A 1590 ASN cc_start: 0.8500 (t0) cc_final: 0.8279 (t0) REVERT: A 1879 PHE cc_start: 0.9029 (m-80) cc_final: 0.8641 (m-10) REVERT: A 1979 MET cc_start: 0.7662 (mmm) cc_final: 0.7338 (mmm) outliers start: 71 outliers final: 49 residues processed: 216 average time/residue: 0.2161 time to fit residues: 74.4017 Evaluate side-chains 207 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1631 THR Chi-restraints excluded: chain A residue 1634 MET Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1868 SER Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.146855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.115077 restraints weight = 37803.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108594 restraints weight = 31861.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109821 restraints weight = 30481.679| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14572 Z= 0.306 Angle : 0.786 12.362 19822 Z= 0.387 Chirality : 0.046 0.260 2258 Planarity : 0.005 0.057 2544 Dihedral : 5.301 29.465 2004 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.51 % Allowed : 26.18 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1826 helix: -0.06 (0.17), residues: 960 sheet: -2.23 (0.36), residues: 195 loop : -2.19 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1965 HIS 0.010 0.002 HIS A1887 PHE 0.030 0.002 PHE A1282 TYR 0.021 0.002 TYR A1591 ARG 0.006 0.001 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 689) hydrogen bonds : angle 5.19949 ( 2007) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.90309 ( 10) covalent geometry : bond 0.00690 (14567) covalent geometry : angle 0.78602 (19812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 153 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.9158 (mmm) cc_final: 0.8823 (tpp) REVERT: A 192 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7682 (pp30) REVERT: A 577 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8871 (pp) REVERT: A 870 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6797 (p-80) REVERT: A 880 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7292 (mmm-85) REVERT: A 1879 PHE cc_start: 0.9012 (m-80) cc_final: 0.8632 (m-10) REVERT: A 1979 MET cc_start: 0.7475 (mmm) cc_final: 0.6602 (mmm) REVERT: A 2056 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7091 (ptm-80) outliers start: 98 outliers final: 65 residues processed: 235 average time/residue: 0.2286 time to fit residues: 84.2492 Evaluate side-chains 211 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 142 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1487 VAL Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1631 THR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2026 VAL Chi-restraints excluded: chain A residue 2056 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 182 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120217 restraints weight = 37404.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116818 restraints weight = 28281.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117581 restraints weight = 26151.218| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14572 Z= 0.127 Angle : 0.695 12.421 19822 Z= 0.331 Chirality : 0.042 0.250 2258 Planarity : 0.004 0.057 2544 Dihedral : 4.913 28.832 2004 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.45 % Allowed : 29.04 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1826 helix: 0.25 (0.17), residues: 954 sheet: -2.20 (0.36), residues: 203 loop : -2.00 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1965 HIS 0.010 0.001 HIS A1887 PHE 0.038 0.002 PHE A1584 TYR 0.022 0.001 TYR A1591 ARG 0.004 0.000 ARG A2002 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 689) hydrogen bonds : angle 4.89151 ( 2007) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.61496 ( 10) covalent geometry : bond 0.00287 (14567) covalent geometry : angle 0.69512 (19812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 1.484 Fit side-chains REVERT: A 16 MET cc_start: 0.9060 (mmm) cc_final: 0.8749 (tpp) REVERT: A 192 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7624 (pp30) REVERT: A 511 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 577 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 588 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7905 (mtm-85) REVERT: A 870 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6646 (p-80) REVERT: A 967 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7426 (m) REVERT: A 1590 ASN cc_start: 0.8076 (t0) cc_final: 0.7786 (t0) REVERT: A 1879 PHE cc_start: 0.8679 (m-80) cc_final: 0.8337 (m-10) outliers start: 67 outliers final: 45 residues processed: 211 average time/residue: 0.2152 time to fit residues: 71.6763 Evaluate side-chains 205 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1418 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102859 restraints weight = 37671.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102627 restraints weight = 26572.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102379 restraints weight = 19563.279| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14572 Z= 0.262 Angle : 0.769 12.187 19822 Z= 0.372 Chirality : 0.045 0.288 2258 Planarity : 0.005 0.054 2544 Dihedral : 5.093 29.251 2004 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.92 % Allowed : 28.77 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1826 helix: 0.15 (0.17), residues: 953 sheet: -2.23 (0.36), residues: 195 loop : -2.10 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1965 HIS 0.012 0.001 HIS A1887 PHE 0.032 0.002 PHE A2037 TYR 0.019 0.002 TYR A1591 ARG 0.008 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 689) hydrogen bonds : angle 5.06826 ( 2007) SS BOND : bond 0.00467 ( 5) SS BOND : angle 0.73992 ( 10) covalent geometry : bond 0.00596 (14567) covalent geometry : angle 0.76881 (19812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.9218 (mmm) cc_final: 0.9004 (tpt) REVERT: A 192 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7732 (pp30) REVERT: A 572 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: A 577 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8864 (pp) REVERT: A 870 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6831 (p-80) REVERT: A 880 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7464 (mmm-85) REVERT: A 892 LEU cc_start: 0.9081 (mm) cc_final: 0.8876 (mm) REVERT: A 1590 ASN cc_start: 0.8606 (t0) cc_final: 0.8319 (t0) REVERT: A 1635 TYR cc_start: 0.8472 (m-80) cc_final: 0.8146 (m-80) REVERT: A 1879 PHE cc_start: 0.9052 (m-80) cc_final: 0.8708 (m-10) REVERT: A 1979 MET cc_start: 0.6867 (mmm) cc_final: 0.6101 (mmm) outliers start: 74 outliers final: 57 residues processed: 212 average time/residue: 0.2117 time to fit residues: 70.6452 Evaluate side-chains 212 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1470 SER Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1992 CYS Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Chi-restraints excluded: chain A residue 2089 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 182 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 0.2980 chunk 8 optimal weight: 0.0370 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1518 ASN A1569 GLN A1752 GLN A1966 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.152649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.120864 restraints weight = 37536.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.117802 restraints weight = 27896.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.118637 restraints weight = 23084.551| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14572 Z= 0.119 Angle : 0.718 12.014 19822 Z= 0.335 Chirality : 0.042 0.254 2258 Planarity : 0.004 0.058 2544 Dihedral : 4.717 26.456 2004 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.32 % Allowed : 30.37 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1826 helix: 0.44 (0.17), residues: 953 sheet: -2.02 (0.36), residues: 200 loop : -1.92 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1628 HIS 0.010 0.001 HIS A1887 PHE 0.027 0.002 PHE A1584 TYR 0.021 0.001 TYR A1591 ARG 0.006 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 689) hydrogen bonds : angle 4.74273 ( 2007) SS BOND : bond 0.00230 ( 5) SS BOND : angle 0.55170 ( 10) covalent geometry : bond 0.00260 (14567) covalent geometry : angle 0.71823 (19812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.514 Fit side-chains REVERT: A 16 MET cc_start: 0.9058 (mmm) cc_final: 0.8748 (tpp) REVERT: A 192 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7673 (pp30) REVERT: A 588 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7784 (mtm-85) REVERT: A 870 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6681 (p-80) REVERT: A 944 MET cc_start: 0.7647 (tmm) cc_final: 0.7209 (tmm) REVERT: A 1590 ASN cc_start: 0.8212 (t0) cc_final: 0.7923 (t0) REVERT: A 1869 MET cc_start: 0.1020 (ttt) cc_final: 0.0804 (ttt) REVERT: A 1879 PHE cc_start: 0.8754 (m-80) cc_final: 0.8398 (m-10) REVERT: A 1979 MET cc_start: 0.6306 (mmm) cc_final: 0.5773 (mmm) REVERT: A 1985 MET cc_start: 0.7060 (pmm) cc_final: 0.6818 (pmm) outliers start: 50 outliers final: 36 residues processed: 204 average time/residue: 0.2129 time to fit residues: 69.4995 Evaluate side-chains 196 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1418 SER Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1992 CYS Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 119 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.150902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.119901 restraints weight = 37643.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.116727 restraints weight = 40399.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118337 restraints weight = 36310.663| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14572 Z= 0.146 Angle : 0.710 12.186 19822 Z= 0.333 Chirality : 0.043 0.279 2258 Planarity : 0.005 0.067 2544 Dihedral : 4.674 28.483 2004 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.86 % Allowed : 30.90 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1826 helix: 0.49 (0.17), residues: 953 sheet: -1.92 (0.37), residues: 193 loop : -1.94 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1965 HIS 0.012 0.001 HIS A1887 PHE 0.030 0.002 PHE A2037 TYR 0.018 0.001 TYR A1591 ARG 0.005 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 689) hydrogen bonds : angle 4.76898 ( 2007) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.57120 ( 10) covalent geometry : bond 0.00337 (14567) covalent geometry : angle 0.70966 (19812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.618 Fit side-chains REVERT: A 16 MET cc_start: 0.9048 (mmm) cc_final: 0.8710 (tpp) REVERT: A 192 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7629 (pp30) REVERT: A 588 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7937 (mtm-85) REVERT: A 870 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6589 (p-80) REVERT: A 944 MET cc_start: 0.7661 (tmm) cc_final: 0.7258 (tmm) REVERT: A 1590 ASN cc_start: 0.7840 (t0) cc_final: 0.7616 (t0) REVERT: A 1749 LEU cc_start: 0.8786 (tt) cc_final: 0.8531 (tp) REVERT: A 1879 PHE cc_start: 0.8479 (m-80) cc_final: 0.8259 (m-10) REVERT: A 1979 MET cc_start: 0.6005 (mmm) cc_final: 0.5704 (mmm) outliers start: 43 outliers final: 37 residues processed: 194 average time/residue: 0.2171 time to fit residues: 67.3409 Evaluate side-chains 197 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1992 CYS Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 158 optimal weight: 0.0670 chunk 128 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1966 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.151667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120096 restraints weight = 37551.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.116212 restraints weight = 32282.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116596 restraints weight = 30900.756| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14572 Z= 0.122 Angle : 0.711 12.511 19822 Z= 0.330 Chirality : 0.042 0.280 2258 Planarity : 0.004 0.066 2544 Dihedral : 4.583 27.613 2004 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 31.03 % Favored : 66.18 % 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: -0.93 (0.20), residues: 1826 helix: 0.57 (0.18), residues: 956 sheet: -1.78 (0.38), residues: 188 loop : -1.94 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1965 HIS 0.010 0.001 HIS A1887 PHE 0.027 0.001 PHE A2037 TYR 0.020 0.001 TYR A 560 ARG 0.005 0.000 ARG A 880 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 689) hydrogen bonds : angle 4.68756 ( 2007) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.50384 ( 10) covalent geometry : bond 0.00279 (14567) covalent geometry : angle 0.71107 (19812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.9105 (mmm) cc_final: 0.8765 (tpp) REVERT: A 192 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7691 (pp30) REVERT: A 588 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7859 (mtm-85) REVERT: A 870 HIS cc_start: 0.6893 (OUTLIER) cc_final: 0.6688 (p-80) REVERT: A 944 MET cc_start: 0.7578 (tmm) cc_final: 0.7202 (tmm) REVERT: A 1557 LEU cc_start: 0.8437 (pp) cc_final: 0.8195 (pp) REVERT: A 1590 ASN cc_start: 0.8162 (t0) cc_final: 0.7911 (t0) REVERT: A 1635 TYR cc_start: 0.8144 (m-80) cc_final: 0.7878 (m-80) REVERT: A 1869 MET cc_start: 0.1095 (ttt) cc_final: 0.0819 (ttt) REVERT: A 1879 PHE cc_start: 0.8780 (m-80) cc_final: 0.8521 (m-10) REVERT: A 1979 MET cc_start: 0.6415 (mmm) cc_final: 0.5903 (mmm) REVERT: A 1985 MET cc_start: 0.6864 (pmm) cc_final: 0.6652 (pmm) outliers start: 42 outliers final: 37 residues processed: 189 average time/residue: 0.2199 time to fit residues: 66.3700 Evaluate side-chains 192 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 ARG Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1841 THR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1992 CYS Chi-restraints excluded: chain A residue 1999 VAL Chi-restraints excluded: chain A residue 2020 HIS Chi-restraints excluded: chain A residue 2026 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 20.0000 chunk 172 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.150973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.119715 restraints weight = 37844.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.114492 restraints weight = 31228.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115250 restraints weight = 26554.358| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14572 Z= 0.146 Angle : 0.723 12.320 19822 Z= 0.337 Chirality : 0.043 0.273 2258 Planarity : 0.004 0.056 2544 Dihedral : 4.593 26.355 2004 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.79 % Allowed : 31.36 % Favored : 65.85 % 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: -0.95 (0.20), residues: 1826 helix: 0.56 (0.17), residues: 956 sheet: -1.79 (0.38), residues: 182 loop : -1.97 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1965 HIS 0.012 0.001 HIS A1887 PHE 0.026 0.002 PHE A2037 TYR 0.017 0.001 TYR A1591 ARG 0.003 0.000 ARG A2002 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 689) hydrogen bonds : angle 4.72491 ( 2007) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.53333 ( 10) covalent geometry : bond 0.00335 (14567) covalent geometry : angle 0.72308 (19812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4139.98 seconds wall clock time: 73 minutes 32.69 seconds (4412.69 seconds total)