Starting phenix.real_space_refine (version: dev) on Sun Feb 19 12:06:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjb_22205/02_2023/6xjb_22205.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Process input model Symmetric amino acids flipped Residue "A GLU 681": "OE1" <-> "OE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1235": "OE1" <-> "OE2" Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1247": "NH1" <-> "NH2" Residue "A PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "A TYR 1321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A GLU 1423": "OE1" <-> "OE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A PHE 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1524": "NH1" <-> "NH2" Residue "A ASP 1555": "OD1" <-> "OD2" Residue "A TYR 1580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1595": "OD1" <-> "OD2" Residue "A TYR 1602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1605": "OE1" <-> "OE2" Residue "A ASP 1609": "OD1" <-> "OD2" Residue "A ARG 1621": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A PHE 1630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1669": "OD1" <-> "OD2" Residue "A TYR 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1698": "OE1" <-> "OE2" Residue "A ARG 1716": "NH1" <-> "NH2" Residue "A PHE 1752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1773": "NH1" <-> "NH2" Residue "A TYR 1826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1850": "OE1" <-> "OE2" Residue "A PHE 1867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1875": "NH1" <-> "NH2" Residue "A PHE 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1907": "OE1" <-> "OE2" Residue "A ASP 1913": "OD1" <-> "OD2" Residue "A PHE 1954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1955": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10070 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10070 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 33, 'TRANS': 1243} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.90, per 1000 atoms: 0.59 Number of scatterers: 10070 At special positions: 0 Unit cell: (94.176, 110.592, 125.28, 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 18 16.00 O 1989 8.00 N 1711 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 17 sheets defined 33.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 782 through 793 removed outlier: 3.807A pdb=" N LYS A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 removed outlier: 4.326A pdb=" N GLY A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1083 removed outlier: 3.718A pdb=" N VAL A1082 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A1083 " --> pdb=" O GLN A1080 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1079 through 1083' Processing helix chain 'A' and resid 1119 through 1128 removed outlier: 3.593A pdb=" N LYS A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1143 Processing helix chain 'A' and resid 1169 through 1174 Processing helix chain 'A' and resid 1211 through 1213 No H-bonds generated for 'chain 'A' and resid 1211 through 1213' Processing helix chain 'A' and resid 1224 through 1238 removed outlier: 4.173A pdb=" N ILE A1228 " --> pdb=" O ASP A1224 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Proline residue: A1234 - end of helix removed outlier: 3.598A pdb=" N LYS A1238 " --> pdb=" O PRO A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 3.540A pdb=" N ARG A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1273 Processing helix chain 'A' and resid 1273 through 1286 removed outlier: 3.935A pdb=" N SER A1277 " --> pdb=" O ASN A1273 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1306 removed outlier: 4.482A pdb=" N ARG A1296 " --> pdb=" O ASN A1292 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1330 through 1335 removed outlier: 3.640A pdb=" N MET A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1357 Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1367 through 1375 removed outlier: 3.537A pdb=" N TYR A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A1373 " --> pdb=" O VAL A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1396 Processing helix chain 'A' and resid 1401 through 1410 Processing helix chain 'A' and resid 1421 through 1430 removed outlier: 3.501A pdb=" N GLY A1429 " --> pdb=" O LYS A1425 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1430 " --> pdb=" O THR A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1444 Processing helix chain 'A' and resid 1450 through 1452 No H-bonds generated for 'chain 'A' and resid 1450 through 1452' Processing helix chain 'A' and resid 1453 through 1459 removed outlier: 3.533A pdb=" N THR A1459 " --> pdb=" O LEU A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1482 No H-bonds generated for 'chain 'A' and resid 1480 through 1482' Processing helix chain 'A' and resid 1491 through 1519 removed outlier: 3.521A pdb=" N ASP A1495 " --> pdb=" O LYS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1527 Processing helix chain 'A' and resid 1558 through 1564 Processing helix chain 'A' and resid 1595 through 1610 removed outlier: 3.864A pdb=" N ALA A1599 " --> pdb=" O ASP A1595 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A1600 " --> pdb=" O LYS A1596 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1601 " --> pdb=" O ASP A1597 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS A1604 " --> pdb=" O ILE A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 removed outlier: 3.552A pdb=" N LYS A1632 " --> pdb=" O GLU A1628 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A1633 " --> pdb=" O PHE A1629 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1628 through 1633' Processing helix chain 'A' and resid 1658 through 1662 removed outlier: 3.564A pdb=" N GLU A1661 " --> pdb=" O ASP A1658 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A1662 " --> pdb=" O SER A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1662' Processing helix chain 'A' and resid 1676 through 1705 Processing helix chain 'A' and resid 1707 through 1714 removed outlier: 3.628A pdb=" N ALA A1713 " --> pdb=" O TYR A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1749 removed outlier: 3.530A pdb=" N ASN A1748 " --> pdb=" O ALA A1744 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1758 removed outlier: 3.546A pdb=" N ILE A1756 " --> pdb=" O PHE A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1798 through 1812 removed outlier: 3.679A pdb=" N ARG A1803 " --> pdb=" O LEU A1799 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1823 Processing helix chain 'A' and resid 1826 through 1834 Processing helix chain 'A' and resid 1848 through 1857 Processing helix chain 'A' and resid 1863 through 1880 Processing helix chain 'A' and resid 1904 through 1921 removed outlier: 3.656A pdb=" N LEU A1908 " --> pdb=" O ASN A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1951 removed outlier: 3.652A pdb=" N THR A1951 " --> pdb=" O TYR A1947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 680 through 681 removed outlier: 6.262A pdb=" N LEU A 680 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 756 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.895A pdb=" N ARG A 699 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 736 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 743 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 765 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.895A pdb=" N ARG A 699 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 797 through 799 removed outlier: 6.043A pdb=" N TYR A 798 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR A 853 " --> pdb=" O ILE A 828 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 804 through 805 removed outlier: 6.831A pdb=" N LEU A 804 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 860 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 858 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP A 889 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 860 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 891 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 862 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 893 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 864 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 920 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 892 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE A 919 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP A 986 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER A 956 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 804 through 805 removed outlier: 6.831A pdb=" N LEU A 804 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 860 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 858 " --> pdb=" O HIS A 887 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP A 889 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 860 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 891 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL A 862 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA A 893 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 864 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 848 through 849 removed outlier: 6.935A pdb=" N ASN A 875 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 870 through 871 removed outlier: 6.412A pdb=" N ILE A 870 " --> pdb=" O GLY A 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884 removed outlier: 6.353A pdb=" N ILE A 883 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE A 945 " --> pdb=" O GLN A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 930 through 931 Processing sheet with id=AB2, first strand: chain 'A' and resid 1053 through 1055 Processing sheet with id=AB3, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 3.765A pdb=" N LYS A1196 " --> pdb=" O ASN A1208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1324 through 1325 Processing sheet with id=AB5, first strand: chain 'A' and resid 1413 through 1417 removed outlier: 3.696A pdb=" N GLU A1417 " --> pdb=" O SER A1469 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1533 through 1534 removed outlier: 7.413A pdb=" N TYR A1534 " --> pdb=" O TYR A1588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1734 through 1739 Processing sheet with id=AB8, first strand: chain 'A' and resid 1836 through 1839 323 hydrogen bonds defined for protein. 927 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: 4.14 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3333 1.34 - 1.46: 1781 1.46 - 1.57: 5109 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 10259 Sorted by residual: bond pdb=" N THR A1057 " pdb=" CA THR A1057 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.72e+00 bond pdb=" N THR A1901 " pdb=" CA THR A1901 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" N VAL A1568 " pdb=" CA VAL A1568 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.07e+00 bond pdb=" N ALA A1113 " pdb=" CA ALA A1113 " ideal model delta sigma weight residual 1.459 1.470 -0.012 1.16e-02 7.43e+03 1.04e+00 bond pdb=" N PRO A1098 " pdb=" CA PRO A1098 " ideal model delta sigma weight residual 1.471 1.459 0.013 1.29e-02 6.01e+03 9.55e-01 ... (remaining 10254 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.28: 211 107.28 - 113.97: 5763 113.97 - 120.65: 4224 120.65 - 127.34: 3597 127.34 - 134.03: 70 Bond angle restraints: 13865 Sorted by residual: angle pdb=" N PRO A1094 " pdb=" CA PRO A1094 " pdb=" CB PRO A1094 " ideal model delta sigma weight residual 103.27 110.21 -6.94 9.00e-01 1.23e+00 5.94e+01 angle pdb=" N PRO A1090 " pdb=" CA PRO A1090 " pdb=" CB PRO A1090 " ideal model delta sigma weight residual 103.33 110.44 -7.11 9.30e-01 1.16e+00 5.84e+01 angle pdb=" N PRO A1098 " pdb=" CA PRO A1098 " pdb=" CB PRO A1098 " ideal model delta sigma weight residual 103.44 110.07 -6.63 1.12e+00 7.97e-01 3.50e+01 angle pdb=" C TYR A1928 " pdb=" CA TYR A1928 " pdb=" CB TYR A1928 " ideal model delta sigma weight residual 115.79 110.30 5.49 1.19e+00 7.06e-01 2.13e+01 angle pdb=" C PRO A1670 " pdb=" N THR A1671 " pdb=" CA THR A1671 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 ... (remaining 13860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5634 17.56 - 35.12: 433 35.12 - 52.68: 76 52.68 - 70.25: 17 70.25 - 87.81: 7 Dihedral angle restraints: 6167 sinusoidal: 2437 harmonic: 3730 Sorted by residual: dihedral pdb=" CA ASP A1669 " pdb=" CB ASP A1669 " pdb=" CG ASP A1669 " pdb=" OD1 ASP A1669 " ideal model delta sinusoidal sigma weight residual -30.00 -88.11 58.11 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A1609 " pdb=" CB ASP A1609 " pdb=" CG ASP A1609 " pdb=" OD1 ASP A1609 " ideal model delta sinusoidal sigma weight residual -30.00 -87.98 57.98 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU A1850 " pdb=" CG GLU A1850 " pdb=" CD GLU A1850 " pdb=" OE1 GLU A1850 " ideal model delta sinusoidal sigma weight residual 0.00 87.81 -87.81 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1209 0.045 - 0.091: 242 0.091 - 0.136: 67 0.136 - 0.181: 2 0.181 - 0.226: 3 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA PRO A1098 " pdb=" N PRO A1098 " pdb=" C PRO A1098 " pdb=" CB PRO A1098 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO A1090 " pdb=" N PRO A1090 " pdb=" C PRO A1090 " pdb=" CB PRO A1090 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO A1094 " pdb=" N PRO A1094 " pdb=" C PRO A1094 " pdb=" CB PRO A1094 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1520 not shown) Planarity restraints: 1803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 707 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 708 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1892 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A1893 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A1893 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1893 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1879 " -0.010 2.00e-02 2.50e+03 9.58e-03 1.61e+00 pdb=" CG PHE A1879 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A1879 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1879 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1879 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1879 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A1879 " 0.001 2.00e-02 2.50e+03 ... (remaining 1800 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 296 2.71 - 3.26: 10494 3.26 - 3.81: 15967 3.81 - 4.35: 20478 4.35 - 4.90: 34592 Nonbonded interactions: 81827 Sorted by model distance: nonbonded pdb=" O GLU A1059 " pdb=" ND2 ASN A1575 " model vdw 2.165 2.520 nonbonded pdb=" OG1 THR A 881 " pdb=" OG SER A 908 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A1707 " pdb=" OE1 GLN A1710 " model vdw 2.218 2.440 nonbonded pdb=" O ASN A 793 " pdb=" OH TYR A 798 " model vdw 2.248 2.440 nonbonded pdb=" O SER A1751 " pdb=" OG SER A1754 " model vdw 2.258 2.440 ... (remaining 81822 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 6352 2.51 5 N 1711 2.21 5 O 1989 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.010 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: 8.740 Check model and map are aligned: 0.140 Process input model: 29.460 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 10259 Z= 0.158 Angle : 0.561 8.428 13865 Z= 0.357 Chirality : 0.040 0.226 1523 Planarity : 0.003 0.037 1803 Dihedral : 13.114 87.806 3787 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.20), residues: 1273 helix: -1.26 (0.22), residues: 406 sheet: -1.53 (0.37), residues: 174 loop : -2.73 (0.19), residues: 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2617 time to fit residues: 55.1817 Evaluate side-chains 67 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 868 ASN A1337 HIS ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1832 GLN A1884 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.097 10259 Z= 0.509 Angle : 0.741 9.013 13865 Z= 0.392 Chirality : 0.047 0.156 1523 Planarity : 0.005 0.073 1803 Dihedral : 5.140 21.975 1394 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.22), residues: 1273 helix: -0.18 (0.25), residues: 413 sheet: -1.36 (0.36), residues: 185 loop : -2.52 (0.21), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 68 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 97 average time/residue: 0.2279 time to fit residues: 32.4514 Evaluate side-chains 78 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 53 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1012 time to fit residues: 6.3060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 124 optimal weight: 0.0010 chunk 102 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 ASN A1337 HIS ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1608 HIS ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 10259 Z= 0.155 Angle : 0.539 6.915 13865 Z= 0.286 Chirality : 0.040 0.153 1523 Planarity : 0.003 0.049 1803 Dihedral : 4.603 19.518 1394 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1273 helix: 0.31 (0.26), residues: 412 sheet: -1.04 (0.38), residues: 166 loop : -2.38 (0.20), residues: 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 94 average time/residue: 0.2300 time to fit residues: 31.5547 Evaluate side-chains 73 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1346 time to fit residues: 3.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10259 Z= 0.189 Angle : 0.536 8.986 13865 Z= 0.284 Chirality : 0.040 0.139 1523 Planarity : 0.003 0.051 1803 Dihedral : 4.564 20.076 1394 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1273 helix: 0.50 (0.26), residues: 412 sheet: -1.00 (0.36), residues: 193 loop : -2.39 (0.21), residues: 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.2390 time to fit residues: 29.2214 Evaluate side-chains 75 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1081 time to fit residues: 4.0677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1337 HIS ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 HIS A1666 GLN ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 10259 Z= 0.382 Angle : 0.637 8.983 13865 Z= 0.336 Chirality : 0.043 0.142 1523 Planarity : 0.004 0.070 1803 Dihedral : 4.957 22.147 1394 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1273 helix: 0.58 (0.26), residues: 407 sheet: -0.95 (0.38), residues: 179 loop : -2.35 (0.21), residues: 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 89 average time/residue: 0.2377 time to fit residues: 30.9575 Evaluate side-chains 76 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1024 time to fit residues: 5.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1337 HIS ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 10259 Z= 0.158 Angle : 0.533 9.892 13865 Z= 0.283 Chirality : 0.040 0.140 1523 Planarity : 0.003 0.049 1803 Dihedral : 4.637 19.813 1394 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1273 helix: 0.76 (0.27), residues: 405 sheet: -0.90 (0.36), residues: 194 loop : -2.29 (0.21), residues: 674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 81 average time/residue: 0.2426 time to fit residues: 28.7097 Evaluate side-chains 67 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1139 time to fit residues: 3.1085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1237 GLN A1337 HIS A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10259 Z= 0.195 Angle : 0.545 10.233 13865 Z= 0.288 Chirality : 0.040 0.153 1523 Planarity : 0.003 0.053 1803 Dihedral : 4.588 19.830 1394 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.23), residues: 1273 helix: 0.76 (0.27), residues: 406 sheet: -0.87 (0.36), residues: 194 loop : -2.27 (0.21), residues: 673 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.2553 time to fit residues: 28.3333 Evaluate side-chains 60 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1020 time to fit residues: 2.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 ASN A1337 HIS A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10259 Z= 0.182 Angle : 0.559 10.639 13865 Z= 0.293 Chirality : 0.040 0.149 1523 Planarity : 0.003 0.050 1803 Dihedral : 4.533 19.599 1394 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1273 helix: 0.71 (0.26), residues: 406 sheet: -0.78 (0.37), residues: 193 loop : -2.25 (0.21), residues: 674 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 78 average time/residue: 0.2411 time to fit residues: 27.9039 Evaluate side-chains 64 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1017 time to fit residues: 3.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1337 HIS A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10259 Z= 0.185 Angle : 0.575 11.040 13865 Z= 0.296 Chirality : 0.041 0.176 1523 Planarity : 0.003 0.050 1803 Dihedral : 4.516 19.522 1394 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1273 helix: 0.71 (0.26), residues: 406 sheet: -0.69 (0.37), residues: 193 loop : -2.21 (0.22), residues: 674 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.2702 time to fit residues: 25.6312 Evaluate side-chains 63 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1679 time to fit residues: 2.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 83 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1051 ASN A1367 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10259 Z= 0.157 Angle : 0.560 11.372 13865 Z= 0.288 Chirality : 0.040 0.191 1523 Planarity : 0.003 0.047 1803 Dihedral : 4.411 19.068 1394 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1273 helix: 0.81 (0.26), residues: 404 sheet: -0.60 (0.37), residues: 193 loop : -2.19 (0.22), residues: 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2600 time to fit residues: 27.1863 Evaluate side-chains 63 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1097 time to fit residues: 2.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 879 ASN ** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.064012 restraints weight = 29704.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066264 restraints weight = 15077.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067801 restraints weight = 9425.722| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10259 Z= 0.218 Angle : 0.585 11.402 13865 Z= 0.301 Chirality : 0.041 0.190 1523 Planarity : 0.003 0.051 1803 Dihedral : 4.468 19.635 1394 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1273 helix: 0.91 (0.27), residues: 402 sheet: -0.65 (0.36), residues: 205 loop : -2.19 (0.22), residues: 666 =============================================================================== Job complete usr+sys time: 1884.52 seconds wall clock time: 35 minutes 40.69 seconds (2140.69 seconds total)