Starting phenix.real_space_refine on Thu Sep 18 05:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y1o_38841/09_2025/8y1o_38841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y1o_38841/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8y1o_38841/09_2025/8y1o_38841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y1o_38841/09_2025/8y1o_38841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y1o_38841/09_2025/8y1o_38841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y1o_38841/09_2025/8y1o_38841.map" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.32, per 1000 atoms: 0.23 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: 1.11 Conformation dependent library (CDL) restraints added in 631.4 milliseconds Enol-peptide restraints added in 2.4 microseconds 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: 0.65 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: 3.16 Time building geometry restraints manager: 1.52 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.850 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- 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 : 9.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.027 0.001 ARG A 880 TYR 0.041 0.002 TYR A1591 PHE 0.045 0.003 PHE A1963 TRP 0.042 0.002 TRP A1965 HIS 0.012 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00544 (14567) covalent geometry : angle 1.07641 (19812) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.77425 ( 10) hydrogen bonds : bond 0.14434 ( 689) hydrogen bonds : angle 6.93585 ( 2007) *********************** 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 : 0.519 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: 0.1004 time to fit residues: 24.4791 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.153473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122437 restraints weight = 37437.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120402 restraints weight = 31397.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.121021 restraints weight = 23141.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121548 restraints weight = 17791.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121711 restraints weight = 15760.735| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14572 Z= 0.133 Angle : 0.663 11.184 19822 Z= 0.325 Chirality : 0.041 0.206 2258 Planarity : 0.005 0.072 2544 Dihedral : 5.067 25.403 2004 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.12 % Allowed : 26.84 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.19), residues: 1826 helix: -0.37 (0.17), residues: 956 sheet: -1.89 (0.36), residues: 204 loop : -2.24 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 880 TYR 0.019 0.001 TYR A1591 PHE 0.028 0.002 PHE A1963 TRP 0.032 0.001 TRP A1965 HIS 0.005 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00284 (14567) covalent geometry : angle 0.66272 (19812) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.49544 ( 10) hydrogen bonds : bond 0.04015 ( 689) hydrogen bonds : angle 5.19621 ( 2007) *********************** 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 212 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 967 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7573 (m) REVERT: A 998 LEU cc_start: 0.8783 (mt) cc_final: 0.8569 (mt) REVERT: A 1386 ASN cc_start: 0.6894 (OUTLIER) cc_final: 0.5999 (t0) REVERT: A 1590 ASN cc_start: 0.7825 (t0) cc_final: 0.7611 (t0) outliers start: 47 outliers final: 23 residues processed: 199 average time/residue: 0.0969 time to fit residues: 31.1370 Evaluate side-chains 176 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 61 LEU 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 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 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 1386 ASN Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1634 MET 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 0 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 180 optimal weight: 0.3980 chunk 96 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.153788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123209 restraints weight = 37401.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.121333 restraints weight = 34736.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122040 restraints weight = 26276.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.122572 restraints weight = 20732.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.122754 restraints weight = 17928.313| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14572 Z= 0.118 Angle : 0.658 11.560 19822 Z= 0.313 Chirality : 0.041 0.221 2258 Planarity : 0.004 0.065 2544 Dihedral : 4.792 27.278 2004 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.46 % Allowed : 26.38 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1826 helix: -0.01 (0.17), residues: 961 sheet: -1.85 (0.36), residues: 204 loop : -2.12 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 880 TYR 0.018 0.001 TYR A1591 PHE 0.051 0.001 PHE A1584 TRP 0.035 0.001 TRP A1965 HIS 0.012 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00266 (14567) covalent geometry : angle 0.65838 (19812) SS BOND : bond 0.00198 ( 5) SS BOND : angle 0.44142 ( 10) hydrogen bonds : bond 0.03538 ( 689) hydrogen bonds : angle 4.90043 ( 2007) *********************** 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 219 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9127 (mmm) cc_final: 0.8817 (tpp) REVERT: A 577 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8763 (pp) REVERT: A 967 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7460 (m) REVERT: A 971 ASP cc_start: 0.7384 (t0) cc_final: 0.6969 (p0) REVERT: A 998 LEU cc_start: 0.8763 (mt) cc_final: 0.8548 (mt) REVERT: A 1386 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6243 (t0) REVERT: A 1590 ASN cc_start: 0.7838 (t0) cc_final: 0.7604 (t0) REVERT: A 1879 PHE cc_start: 0.8509 (m-80) cc_final: 0.8141 (m-10) REVERT: A 1979 MET cc_start: 0.6719 (mmm) cc_final: 0.6104 (mmm) outliers start: 52 outliers final: 24 residues processed: 206 average time/residue: 0.0882 time to fit residues: 29.8980 Evaluate side-chains 184 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 506 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 LEU 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 1386 ASN 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 1841 THR Chi-restraints excluded: chain A residue 1881 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 13 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.150698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.119385 restraints weight = 37934.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115346 restraints weight = 29063.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116062 restraints weight = 24905.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.116214 restraints weight = 18937.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.116373 restraints weight = 17276.516| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14572 Z= 0.201 Angle : 0.699 11.731 19822 Z= 0.337 Chirality : 0.043 0.240 2258 Planarity : 0.005 0.062 2544 Dihedral : 4.817 28.474 2004 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.45 % Allowed : 26.05 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.20), residues: 1826 helix: 0.19 (0.17), residues: 952 sheet: -1.82 (0.37), residues: 194 loop : -2.10 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 880 TYR 0.016 0.001 TYR A1591 PHE 0.029 0.002 PHE A1584 TRP 0.032 0.002 TRP A1965 HIS 0.009 0.001 HIS A2020 Details of bonding type rmsd covalent geometry : bond 0.00457 (14567) covalent geometry : angle 0.69916 (19812) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.61978 ( 10) hydrogen bonds : bond 0.03568 ( 689) hydrogen bonds : angle 4.90924 ( 2007) *********************** 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 228 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9155 (mmm) cc_final: 0.8854 (tpp) REVERT: A 192 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7713 (pp30) REVERT: A 295 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 577 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8791 (pp) REVERT: A 967 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7571 (m) REVERT: A 971 ASP cc_start: 0.7488 (t0) cc_final: 0.6934 (p0) REVERT: A 998 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 1749 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 1868 SER cc_start: 0.3570 (OUTLIER) cc_final: 0.3295 (m) REVERT: A 1879 PHE cc_start: 0.8817 (m-80) cc_final: 0.8421 (m-10) REVERT: A 1979 MET cc_start: 0.7173 (mmm) cc_final: 0.6318 (mmm) outliers start: 67 outliers final: 45 residues processed: 212 average time/residue: 0.0910 time to fit residues: 31.9021 Evaluate side-chains 201 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 42 VAL 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 290 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 564 LEU 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 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 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 902 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 998 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 1388 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 130 optimal weight: 0.0980 chunk 88 optimal weight: 30.0000 chunk 104 optimal weight: 0.0370 chunk 153 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 180 optimal weight: 20.0000 chunk 115 optimal weight: 0.0370 chunk 144 optimal weight: 2.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1590 ASN A1752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.153742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.123576 restraints weight = 37587.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120104 restraints weight = 30462.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120594 restraints weight = 23165.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.120981 restraints weight = 18225.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.121855 restraints weight = 16342.887| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14572 Z= 0.108 Angle : 0.660 11.476 19822 Z= 0.310 Chirality : 0.041 0.239 2258 Planarity : 0.004 0.061 2544 Dihedral : 4.564 27.890 2004 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.06 % Allowed : 27.77 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.20), residues: 1826 helix: 0.42 (0.18), residues: 952 sheet: -1.77 (0.36), residues: 204 loop : -2.00 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.019 0.001 TYR A1591 PHE 0.037 0.001 PHE A1584 TRP 0.037 0.001 TRP A1965 HIS 0.010 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00242 (14567) covalent geometry : angle 0.66018 (19812) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.65273 ( 10) hydrogen bonds : bond 0.03146 ( 689) hydrogen bonds : angle 4.66756 ( 2007) *********************** 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 220 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9113 (mmm) cc_final: 0.8794 (tpp) REVERT: A 192 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7719 (pp30) REVERT: A 577 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 708 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: A 944 MET cc_start: 0.7679 (tmm) cc_final: 0.7109 (tmm) REVERT: A 967 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7564 (m) REVERT: A 1547 SER cc_start: 0.8383 (t) cc_final: 0.8021 (p) REVERT: A 1554 THR cc_start: 0.8809 (m) cc_final: 0.8557 (p) REVERT: A 1698 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7860 (tpp-160) REVERT: A 1749 LEU cc_start: 0.8770 (tt) cc_final: 0.8564 (tp) REVERT: A 1879 PHE cc_start: 0.8601 (m-80) cc_final: 0.8305 (m-10) outliers start: 46 outliers final: 31 residues processed: 206 average time/residue: 0.0961 time to fit residues: 31.8858 Evaluate side-chains 192 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 564 LEU 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 708 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 967 THR 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 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 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 121 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 152 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 180 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.152366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121601 restraints weight = 37345.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.117824 restraints weight = 28790.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118685 restraints weight = 24058.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.118943 restraints weight = 17630.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119299 restraints weight = 16220.784| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1714 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= 0.130 Angle : 0.672 11.628 19822 Z= 0.315 Chirality : 0.041 0.261 2258 Planarity : 0.004 0.061 2544 Dihedral : 4.483 27.368 2004 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.12 % Allowed : 27.24 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.20), residues: 1826 helix: 0.49 (0.17), residues: 952 sheet: -1.79 (0.36), residues: 203 loop : -1.93 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 880 TYR 0.016 0.001 TYR A1591 PHE 0.036 0.001 PHE A1584 TRP 0.035 0.001 TRP A1965 HIS 0.010 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00299 (14567) covalent geometry : angle 0.67158 (19812) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.65348 ( 10) hydrogen bonds : bond 0.03103 ( 689) hydrogen bonds : angle 4.61852 ( 2007) *********************** 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 230 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9138 (mmm) cc_final: 0.8791 (tpp) REVERT: A 192 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7737 (pp30) REVERT: A 577 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8815 (pp) REVERT: A 708 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: A 967 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7404 (m) REVERT: A 1554 THR cc_start: 0.8682 (m) cc_final: 0.8430 (p) REVERT: A 1879 PHE cc_start: 0.8636 (m-80) cc_final: 0.8366 (m-10) REVERT: A 1979 MET cc_start: 0.6152 (mmm) cc_final: 0.5692 (mmm) outliers start: 62 outliers final: 46 residues processed: 219 average time/residue: 0.0957 time to fit residues: 33.6753 Evaluate side-chains 207 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 564 LEU 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 637 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 708 GLU 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 923 LEU 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 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 1284 SER Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1626 TYR Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS Chi-restraints excluded: chain A residue 1735 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 1964 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 84 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1590 ASN A1606 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.153009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.122661 restraints weight = 37236.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119726 restraints weight = 31145.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121401 restraints weight = 24288.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121645 restraints weight = 16878.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122179 restraints weight = 15957.763| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1853 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= 0.113 Angle : 0.670 12.002 19822 Z= 0.312 Chirality : 0.041 0.253 2258 Planarity : 0.004 0.061 2544 Dihedral : 4.402 25.786 2004 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.79 % Allowed : 27.91 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.20), residues: 1826 helix: 0.54 (0.17), residues: 955 sheet: -1.75 (0.37), residues: 197 loop : -1.93 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 880 TYR 0.016 0.001 TYR A1591 PHE 0.038 0.001 PHE A1584 TRP 0.035 0.001 TRP A1965 HIS 0.011 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00259 (14567) covalent geometry : angle 0.66974 (19812) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.54174 ( 10) hydrogen bonds : bond 0.03007 ( 689) hydrogen bonds : angle 4.56530 ( 2007) *********************** 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 225 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9120 (mmm) cc_final: 0.8793 (tpp) REVERT: A 577 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8784 (pp) REVERT: A 708 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: A 880 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6811 (mmm-85) REVERT: A 944 MET cc_start: 0.7511 (tmm) cc_final: 0.7079 (tmm) REVERT: A 967 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7353 (m) REVERT: A 1547 SER cc_start: 0.8397 (t) cc_final: 0.7972 (p) REVERT: A 1554 THR cc_start: 0.8738 (m) cc_final: 0.8358 (p) REVERT: A 1701 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8338 (pt) REVERT: A 1879 PHE cc_start: 0.8346 (m-80) cc_final: 0.8120 (m-10) REVERT: A 1979 MET cc_start: 0.6088 (mmm) cc_final: 0.5779 (mmm) outliers start: 57 outliers final: 42 residues processed: 212 average time/residue: 0.0995 time to fit residues: 33.4510 Evaluate side-chains 207 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 564 LEU 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 637 VAL Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 949 SER 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 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 1359 CYS Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP 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 1881 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1965 TRP Chi-restraints excluded: chain A residue 1988 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 106 optimal weight: 0.0270 chunk 78 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.152537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121210 restraints weight = 37089.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.118043 restraints weight = 28220.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.119253 restraints weight = 23697.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.119433 restraints weight = 16925.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120216 restraints weight = 15563.873| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 0.041 14572 Z= 0.127 Angle : 0.683 12.037 19822 Z= 0.317 Chirality : 0.042 0.283 2258 Planarity : 0.004 0.060 2544 Dihedral : 4.376 25.636 2004 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.79 % Allowed : 28.37 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1826 helix: 0.54 (0.17), residues: 955 sheet: -1.62 (0.38), residues: 187 loop : -1.93 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 880 TYR 0.015 0.001 TYR A1591 PHE 0.037 0.001 PHE A1584 TRP 0.034 0.001 TRP A1965 HIS 0.011 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00294 (14567) covalent geometry : angle 0.68269 (19812) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.53532 ( 10) hydrogen bonds : bond 0.03013 ( 689) hydrogen bonds : angle 4.56662 ( 2007) *********************** 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 218 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9134 (mmm) cc_final: 0.8799 (tpp) REVERT: A 577 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 708 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6613 (tt0) REVERT: A 880 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6824 (mmm-85) REVERT: A 944 MET cc_start: 0.7478 (tmm) cc_final: 0.7023 (tmm) REVERT: A 967 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7399 (m) REVERT: A 1698 ARG cc_start: 0.7816 (mmp-170) cc_final: 0.7335 (mmm160) REVERT: A 1879 PHE cc_start: 0.8502 (m-80) cc_final: 0.8260 (m-10) REVERT: A 1979 MET cc_start: 0.6391 (mmm) cc_final: 0.5985 (mmm) outliers start: 57 outliers final: 43 residues processed: 205 average time/residue: 0.0968 time to fit residues: 32.0063 Evaluate side-chains 206 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 61 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 564 LEU 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 637 VAL Chi-restraints excluded: chain A residue 708 GLU 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 923 LEU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 983 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 1388 SER Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP 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 1881 LEU Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 1988 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 128 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.152951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122487 restraints weight = 37379.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119633 restraints weight = 29868.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.120413 restraints weight = 23625.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120837 restraints weight = 17470.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.121408 restraints weight = 15530.106| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2017 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= 0.119 Angle : 0.683 12.284 19822 Z= 0.316 Chirality : 0.041 0.285 2258 Planarity : 0.004 0.060 2544 Dihedral : 4.349 26.194 2004 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.19 % Allowed : 28.64 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.20), residues: 1826 helix: 0.57 (0.17), residues: 955 sheet: -1.74 (0.37), residues: 197 loop : -1.89 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 880 TYR 0.019 0.001 TYR A 560 PHE 0.038 0.001 PHE A1584 TRP 0.049 0.001 TRP A1965 HIS 0.011 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00275 (14567) covalent geometry : angle 0.68287 (19812) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.50627 ( 10) hydrogen bonds : bond 0.02968 ( 689) hydrogen bonds : angle 4.54334 ( 2007) *********************** 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 212 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.9122 (mmm) cc_final: 0.8790 (tpp) REVERT: A 577 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8727 (pp) REVERT: A 708 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6634 (tt0) REVERT: A 880 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6824 (mmm-85) REVERT: A 944 MET cc_start: 0.7442 (tmm) cc_final: 0.6944 (tmm) REVERT: A 967 THR cc_start: 0.7760 (OUTLIER) cc_final: 0.7421 (m) REVERT: A 1410 ASN cc_start: 0.8293 (t0) cc_final: 0.8054 (t0) REVERT: A 1698 ARG cc_start: 0.7825 (mmp-170) cc_final: 0.7338 (mmm160) REVERT: A 1869 MET cc_start: 0.1708 (ttt) cc_final: 0.1445 (ttt) REVERT: A 1979 MET cc_start: 0.6449 (mmm) cc_final: 0.6051 (mmm) REVERT: A 2090 GLN cc_start: 0.8234 (pm20) cc_final: 0.7892 (pm20) outliers start: 48 outliers final: 39 residues processed: 205 average time/residue: 0.0974 time to fit residues: 31.9991 Evaluate side-chains 200 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 564 LEU 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 637 VAL Chi-restraints excluded: chain A residue 708 GLU 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 880 ARG 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 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 1388 SER Chi-restraints excluded: chain A residue 1409 VAL Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS 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 1964 LEU Chi-restraints excluded: chain A residue 1988 CYS Chi-restraints excluded: chain A residue 1999 VAL 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 55 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.152533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.121861 restraints weight = 37061.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.118165 restraints weight = 27559.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.119223 restraints weight = 23587.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119778 restraints weight = 16289.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.120165 restraints weight = 14987.273| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2101 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= 0.133 Angle : 0.702 12.332 19822 Z= 0.325 Chirality : 0.042 0.282 2258 Planarity : 0.004 0.060 2544 Dihedral : 4.360 26.223 2004 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.99 % Allowed : 28.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1826 helix: 0.59 (0.17), residues: 955 sheet: -1.59 (0.37), residues: 193 loop : -1.89 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 938 TYR 0.015 0.001 TYR A1591 PHE 0.038 0.001 PHE A1584 TRP 0.049 0.001 TRP A1965 HIS 0.011 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00308 (14567) covalent geometry : angle 0.70185 (19812) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.51246 ( 10) hydrogen bonds : bond 0.03025 ( 689) hydrogen bonds : angle 4.55164 ( 2007) ********************** 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 212 residues out of total 1509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.9124 (mmm) cc_final: 0.8788 (tpp) REVERT: A 577 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (pp) REVERT: A 708 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: A 880 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6869 (mmm-85) REVERT: A 944 MET cc_start: 0.7448 (tmm) cc_final: 0.6978 (tmm) REVERT: A 967 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7476 (m) REVERT: A 1698 ARG cc_start: 0.7867 (mmp-170) cc_final: 0.7381 (mmm160) REVERT: A 1979 MET cc_start: 0.6558 (mmm) cc_final: 0.6103 (mmm) REVERT: A 2090 GLN cc_start: 0.8287 (pm20) cc_final: 0.7830 (pm20) outliers start: 45 outliers final: 38 residues processed: 206 average time/residue: 0.0979 time to fit residues: 31.9564 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 : 0.552 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 564 LEU 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 637 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 708 GLU 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 880 ARG 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 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 1388 SER Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1569 GLN Chi-restraints excluded: chain A residue 1586 TRP Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1693 HIS 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 1964 LEU Chi-restraints excluded: chain A residue 1988 CYS Chi-restraints excluded: chain A residue 1999 VAL 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 107 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 50 optimal weight: 0.0050 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.153744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122544 restraints weight = 37264.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.119378 restraints weight = 29133.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.120496 restraints weight = 22896.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.120842 restraints weight = 16766.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.120973 restraints weight = 15299.872| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2180 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= 0.115 Angle : 0.708 12.470 19822 Z= 0.326 Chirality : 0.042 0.282 2258 Planarity : 0.004 0.069 2544 Dihedral : 4.318 26.011 2004 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.86 % Allowed : 29.44 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.20), residues: 1826 helix: 0.63 (0.17), residues: 955 sheet: -1.47 (0.38), residues: 188 loop : -1.85 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 938 TYR 0.016 0.001 TYR A1591 PHE 0.044 0.001 PHE A1584 TRP 0.052 0.001 TRP A1965 HIS 0.010 0.001 HIS A1887 Details of bonding type rmsd covalent geometry : bond 0.00264 (14567) covalent geometry : angle 0.70797 (19812) SS BOND : bond 0.00218 ( 5) SS BOND : angle 0.48313 ( 10) hydrogen bonds : bond 0.02973 ( 689) hydrogen bonds : angle 4.53725 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.60 seconds wall clock time: 38 minutes 49.98 seconds (2329.98 seconds total)