Starting phenix.real_space_refine on Sun Mar 17 01:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyi_28690/03_2024/8eyi_28690_neut_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.150 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 63 5.16 5 C 10307 2.51 5 N 2865 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 2012": "OE1" <-> "OE2" Residue "F GLU 1100": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16252 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 7150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7150 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 47, 'TRANS': 913} Chain breaks: 2 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "F" Number of atoms: 8910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 8910 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 64, 'TRANS': 1146} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 249 Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NDP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.51, per 1000 atoms: 0.52 Number of scatterers: 16252 At special positions: 0 Unit cell: (161.71, 105.06, 156.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 12 15.00 O 3005 8.00 N 2865 7.00 C 10307 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: 6.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3986 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 19 sheets defined 33.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'E' and resid 873 through 877 Processing helix chain 'E' and resid 888 through 903 Processing helix chain 'E' and resid 907 through 909 No H-bonds generated for 'chain 'E' and resid 907 through 909' Processing helix chain 'E' and resid 966 through 969 Processing helix chain 'E' and resid 987 through 997 Processing helix chain 'E' and resid 1026 through 1039 Processing helix chain 'E' and resid 1059 through 1065 removed outlier: 3.660A pdb=" N GLN E1064 " --> pdb=" O ALA E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1424 through 1433 Processing helix chain 'E' and resid 1453 through 1462 removed outlier: 3.718A pdb=" N ARG E1462 " --> pdb=" O ASN E1458 " (cutoff:3.500A) Processing helix chain 'E' and resid 1466 through 1469 No H-bonds generated for 'chain 'E' and resid 1466 through 1469' Processing helix chain 'E' and resid 1491 through 1499 Processing helix chain 'E' and resid 1541 through 1543 No H-bonds generated for 'chain 'E' and resid 1541 through 1543' Processing helix chain 'E' and resid 1550 through 1553 No H-bonds generated for 'chain 'E' and resid 1550 through 1553' Processing helix chain 'E' and resid 1573 through 1580 Processing helix chain 'E' and resid 1585 through 1587 No H-bonds generated for 'chain 'E' and resid 1585 through 1587' Processing helix chain 'E' and resid 1630 through 1632 No H-bonds generated for 'chain 'E' and resid 1630 through 1632' Processing helix chain 'E' and resid 1642 through 1647 removed outlier: 4.392A pdb=" N SER E1647 " --> pdb=" O GLU E1643 " (cutoff:3.500A) Processing helix chain 'E' and resid 1649 through 1659 Processing helix chain 'E' and resid 1679 through 1690 Processing helix chain 'E' and resid 1702 through 1711 Processing helix chain 'E' and resid 1717 through 1719 No H-bonds generated for 'chain 'E' and resid 1717 through 1719' Processing helix chain 'E' and resid 1727 through 1735 Processing helix chain 'E' and resid 1750 through 1758 removed outlier: 3.912A pdb=" N ALA E1755 " --> pdb=" O LYS E1752 " (cutoff:3.500A) Processing helix chain 'E' and resid 1772 through 1775 No H-bonds generated for 'chain 'E' and resid 1772 through 1775' Processing helix chain 'E' and resid 1782 through 1787 Processing helix chain 'E' and resid 1797 through 1799 No H-bonds generated for 'chain 'E' and resid 1797 through 1799' Processing helix chain 'E' and resid 1805 through 1819 removed outlier: 3.616A pdb=" N VAL E1810 " --> pdb=" O ASP E1806 " (cutoff:3.500A) Processing helix chain 'E' and resid 1837 through 1845 Processing helix chain 'E' and resid 1895 through 1906 Processing helix chain 'E' and resid 1923 through 1934 Processing helix chain 'E' and resid 1949 through 1962 removed outlier: 3.539A pdb=" N LEU E1962 " --> pdb=" O GLU E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1985 through 2009 Proline residue: E1994 - end of helix removed outlier: 3.898A pdb=" N SER E1997 " --> pdb=" O LYS E1993 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E1998 " --> pdb=" O PRO E1994 " (cutoff:3.500A) Processing helix chain 'E' and resid 2022 through 2025 No H-bonds generated for 'chain 'E' and resid 2022 through 2025' Processing helix chain 'E' and resid 2032 through 2051 Processing helix chain 'E' and resid 2088 through 2100 removed outlier: 3.845A pdb=" N ASN E2100 " --> pdb=" O ASP E2096 " (cutoff:3.500A) Processing helix chain 'F' and resid 874 through 877 Processing helix chain 'F' and resid 888 through 903 removed outlier: 3.598A pdb=" N LEU F 892 " --> pdb=" O ALA F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 969 Processing helix chain 'F' and resid 987 through 997 Processing helix chain 'F' and resid 1026 through 1039 Processing helix chain 'F' and resid 1059 through 1064 removed outlier: 3.667A pdb=" N GLN F1064 " --> pdb=" O ALA F1060 " (cutoff:3.500A) Processing helix chain 'F' and resid 1132 through 1149 Processing helix chain 'F' and resid 1177 through 1187 Processing helix chain 'F' and resid 1200 through 1209 Proline residue: F1207 - end of helix Processing helix chain 'F' and resid 1222 through 1233 Processing helix chain 'F' and resid 1247 through 1250 No H-bonds generated for 'chain 'F' and resid 1247 through 1250' Processing helix chain 'F' and resid 1256 through 1261 Processing helix chain 'F' and resid 1277 through 1289 removed outlier: 4.407A pdb=" N ALA F1282 " --> pdb=" O ALA F1279 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA F1285 " --> pdb=" O ALA F1282 " (cutoff:3.500A) Processing helix chain 'F' and resid 1305 through 1307 No H-bonds generated for 'chain 'F' and resid 1305 through 1307' Processing helix chain 'F' and resid 1325 through 1335 Processing helix chain 'F' and resid 1352 through 1361 Processing helix chain 'F' and resid 1374 through 1383 Processing helix chain 'F' and resid 1423 through 1433 Processing helix chain 'F' and resid 1453 through 1461 Processing helix chain 'F' and resid 1491 through 1499 Processing helix chain 'F' and resid 1541 through 1543 No H-bonds generated for 'chain 'F' and resid 1541 through 1543' Processing helix chain 'F' and resid 1573 through 1579 Processing helix chain 'F' and resid 1585 through 1587 No H-bonds generated for 'chain 'F' and resid 1585 through 1587' Processing helix chain 'F' and resid 1630 through 1632 No H-bonds generated for 'chain 'F' and resid 1630 through 1632' Processing helix chain 'F' and resid 1642 through 1647 removed outlier: 4.405A pdb=" N SER F1647 " --> pdb=" O GLU F1643 " (cutoff:3.500A) Processing helix chain 'F' and resid 1649 through 1659 Processing helix chain 'F' and resid 1679 through 1690 Processing helix chain 'F' and resid 1702 through 1711 Processing helix chain 'F' and resid 1717 through 1719 No H-bonds generated for 'chain 'F' and resid 1717 through 1719' Processing helix chain 'F' and resid 1726 through 1735 Processing helix chain 'F' and resid 1751 through 1759 Processing helix chain 'F' and resid 1772 through 1775 No H-bonds generated for 'chain 'F' and resid 1772 through 1775' Processing helix chain 'F' and resid 1784 through 1787 Processing helix chain 'F' and resid 1798 through 1800 No H-bonds generated for 'chain 'F' and resid 1798 through 1800' Processing helix chain 'F' and resid 1807 through 1820 Processing helix chain 'F' and resid 1833 through 1843 removed outlier: 5.198A pdb=" N GLU F1837 " --> pdb=" O ALA F1834 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N MET F1843 " --> pdb=" O PHE F1840 " (cutoff:3.500A) Processing helix chain 'F' and resid 1895 through 1906 removed outlier: 3.538A pdb=" N GLU F1899 " --> pdb=" O GLY F1895 " (cutoff:3.500A) Processing helix chain 'F' and resid 1923 through 1934 Processing helix chain 'F' and resid 1949 through 1962 removed outlier: 3.536A pdb=" N LEU F1962 " --> pdb=" O GLU F1958 " (cutoff:3.500A) Processing helix chain 'F' and resid 1980 through 1982 No H-bonds generated for 'chain 'F' and resid 1980 through 1982' Processing helix chain 'F' and resid 1985 through 2009 Proline residue: F1994 - end of helix removed outlier: 3.871A pdb=" N SER F1997 " --> pdb=" O LYS F1993 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY F1998 " --> pdb=" O PRO F1994 " (cutoff:3.500A) Processing helix chain 'F' and resid 2022 through 2025 No H-bonds generated for 'chain 'F' and resid 2022 through 2025' Processing helix chain 'F' and resid 2032 through 2050 Processing helix chain 'F' and resid 2069 through 2072 No H-bonds generated for 'chain 'F' and resid 2069 through 2072' Processing helix chain 'F' and resid 2088 through 2100 removed outlier: 3.840A pdb=" N ASN F2100 " --> pdb=" O ASP F2096 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 860 through 865 removed outlier: 3.682A pdb=" N GLY E 956 " --> pdb=" O PHE E 944 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU E 948 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU E 952 " --> pdb=" O GLU E 948 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU E1010 " --> pdb=" O ARG E1019 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E1021 " --> pdb=" O ILE E1008 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE E1008 " --> pdb=" O LEU E1021 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 1413 through 1416 removed outlier: 5.877A pdb=" N VAL E1472 " --> pdb=" O LEU E1443 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA E1445 " --> pdb=" O VAL E1472 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E1474 " --> pdb=" O ALA E1445 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET E1503 " --> pdb=" O PHE E1514 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E1514 " --> pdb=" O MET E1503 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL E2105 " --> pdb=" O PHE E1117 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E2057 " --> pdb=" O LEU E2106 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER E2108 " --> pdb=" O ALA E2057 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN E2059 " --> pdb=" O SER E2108 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE E1888 " --> pdb=" O GLY E1966 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL E1968 " --> pdb=" O ILE E1888 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA E1890 " --> pdb=" O VAL E1968 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN E1970 " --> pdb=" O ALA E1890 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS E1911 " --> pdb=" O TYR E1887 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE E1889 " --> pdb=" O LYS E1911 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E1913 " --> pdb=" O ILE E1889 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN E1938 " --> pdb=" O LEU E1912 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU E1914 " --> pdb=" O GLN E1938 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN E1940 " --> pdb=" O LEU E1914 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 1525 through 1528 Processing sheet with id= D, first strand: chain 'E' and resid 1531 through 1535 Processing sheet with id= E, first strand: chain 'E' and resid 1625 through 1628 removed outlier: 6.847A pdb=" N SER E1604 " --> pdb=" O TYR E1567 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA E1569 " --> pdb=" O GLU E1602 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLU E1602 " --> pdb=" O ALA E1569 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 1568 through 1571 removed outlier: 4.617A pdb=" N VAL E1852 " --> pdb=" O LEU E1571 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 1790 through 1793 Processing sheet with id= H, first strand: chain 'E' and resid 1047 through 1052 removed outlier: 6.955A pdb=" N HIS E1098 " --> pdb=" O THR E1050 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 860 through 864 removed outlier: 3.535A pdb=" N GLY F 956 " --> pdb=" O PHE F 944 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU F1010 " --> pdb=" O ARG F1019 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU F1021 " --> pdb=" O ILE F1008 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F1008 " --> pdb=" O LEU F1021 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 878 through 880 removed outlier: 3.735A pdb=" N THR F 879 " --> pdb=" O ASP F1000 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 1505 through 1507 removed outlier: 4.334A pdb=" N VAL F2105 " --> pdb=" O PHE F1117 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA F2057 " --> pdb=" O LEU F2106 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER F2108 " --> pdb=" O ALA F2057 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN F2059 " --> pdb=" O SER F2108 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE F1888 " --> pdb=" O GLY F1966 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F1968 " --> pdb=" O ILE F1888 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA F1890 " --> pdb=" O VAL F1968 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN F1970 " --> pdb=" O ALA F1890 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS F1911 " --> pdb=" O TYR F1887 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE F1889 " --> pdb=" O LYS F1911 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F1913 " --> pdb=" O ILE F1889 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN F1938 " --> pdb=" O LEU F1912 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU F1914 " --> pdb=" O GLN F1938 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN F1940 " --> pdb=" O LEU F1914 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 1386 through 1393 removed outlier: 6.798A pdb=" N LEU F1402 " --> pdb=" O VAL F1389 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU F1391 " --> pdb=" O LEU F1400 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU F1400 " --> pdb=" O LEU F1391 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS F1393 " --> pdb=" O SER F1398 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SER F1398 " --> pdb=" O LYS F1393 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN F1316 " --> pdb=" O VAL F1245 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN F1267 " --> pdb=" O MET F1240 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL F1242 " --> pdb=" O GLN F1267 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER F1269 " --> pdb=" O VAL F1242 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU F1244 " --> pdb=" O SER F1269 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F1271 " --> pdb=" O GLU F1244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA F1293 " --> pdb=" O ALA F1272 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASP F1274 " --> pdb=" O ALA F1293 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY F1295 " --> pdb=" O ASP F1274 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 1413 through 1416 Processing sheet with id= N, first strand: chain 'F' and resid 1525 through 1528 Processing sheet with id= O, first strand: chain 'F' and resid 1531 through 1535 Processing sheet with id= P, first strand: chain 'F' and resid 1562 through 1565 Processing sheet with id= Q, first strand: chain 'F' and resid 1828 through 1832 removed outlier: 6.944A pdb=" N LYS F1851 " --> pdb=" O THR F1829 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE F1831 " --> pdb=" O LYS F1851 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F1853 " --> pdb=" O PHE F1831 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL F1852 " --> pdb=" O LEU F1571 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER F1604 " --> pdb=" O TYR F1567 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA F1569 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU F1602 " --> pdb=" O ALA F1569 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 1790 through 1793 removed outlier: 6.577A pdb=" N ARG F1694 " --> pdb=" O LEU F1671 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE F1673 " --> pdb=" O ARG F1694 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE F1696 " --> pdb=" O ILE F1673 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 1047 through 1051 removed outlier: 6.897A pdb=" N HIS F1098 " --> pdb=" O THR F1050 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.52: 11618 1.52 - 1.88: 5011 1.88 - 2.24: 0 2.24 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 16630 Sorted by residual: bond pdb=" C GLU F1802 " pdb=" N ALA F1805 " ideal model delta sigma weight residual 1.332 2.969 -1.637 1.40e-02 5.10e+03 1.37e+04 bond pdb=" C1B NDP F3002 " pdb=" C2B NDP F3002 " ideal model delta sigma weight residual 1.575 1.256 0.319 3.70e-02 7.30e+02 7.45e+01 bond pdb=" C1B NDP E3002 " pdb=" C2B NDP E3002 " ideal model delta sigma weight residual 1.575 1.256 0.319 3.70e-02 7.30e+02 7.43e+01 bond pdb=" C2D NDP F3002 " pdb=" C3D NDP F3002 " ideal model delta sigma weight residual 1.545 1.244 0.301 3.60e-02 7.72e+02 7.00e+01 bond pdb=" C1B NDP E3001 " pdb=" C2B NDP E3001 " ideal model delta sigma weight residual 1.575 1.268 0.307 3.70e-02 7.30e+02 6.90e+01 ... (remaining 16625 not shown) Histogram of bond angle deviations from ideal: 61.67 - 76.30: 1 76.30 - 90.92: 0 90.92 - 105.54: 402 105.54 - 120.17: 14874 120.17 - 134.79: 7441 Bond angle restraints: 22718 Sorted by residual: angle pdb=" O GLU F1802 " pdb=" C GLU F1802 " pdb=" N ALA F1805 " ideal model delta sigma weight residual 122.59 61.67 60.92 1.33e+00 5.65e-01 2.10e+03 angle pdb=" PA NDP F3001 " pdb=" O3 NDP F3001 " pdb=" PN NDP F3001 " ideal model delta sigma weight residual 107.74 128.89 -21.15 1.95e+00 2.62e-01 1.17e+02 angle pdb=" PA NDP F3002 " pdb=" O3 NDP F3002 " pdb=" PN NDP F3002 " ideal model delta sigma weight residual 107.74 126.90 -19.16 1.95e+00 2.62e-01 9.61e+01 angle pdb=" C5B NDP F3002 " pdb=" O5B NDP F3002 " pdb=" PA NDP F3002 " ideal model delta sigma weight residual 103.84 120.19 -16.35 1.91e+00 2.73e-01 7.29e+01 angle pdb=" O1X NDP F3002 " pdb=" P2B NDP F3002 " pdb=" O3X NDP F3002 " ideal model delta sigma weight residual 117.46 107.79 9.67 1.17e+00 7.36e-01 6.88e+01 ... (remaining 22713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 9384 33.22 - 66.44: 324 66.44 - 99.66: 20 99.66 - 132.87: 0 132.87 - 166.09: 2 Dihedral angle restraints: 9730 sinusoidal: 3533 harmonic: 6197 Sorted by residual: dihedral pdb=" CA MET F1332 " pdb=" C MET F1332 " pdb=" N VAL F1333 " pdb=" CA VAL F1333 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" C5B NDP F3001 " pdb=" O5B NDP F3001 " pdb=" PA NDP F3001 " pdb=" O3 NDP F3001 " ideal model delta sinusoidal sigma weight residual 175.04 8.95 166.09 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C5B NDP E3001 " pdb=" O5B NDP E3001 " pdb=" PA NDP E3001 " pdb=" O3 NDP E3001 " ideal model delta sinusoidal sigma weight residual 175.04 19.32 155.72 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2546 0.107 - 0.214: 58 0.214 - 0.320: 7 0.320 - 0.427: 5 0.427 - 0.534: 2 Chirality restraints: 2618 Sorted by residual: chirality pdb=" C2B NDP F3002 " pdb=" C1B NDP F3002 " pdb=" C3B NDP F3002 " pdb=" O2B NDP F3002 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C3D NDP E3001 " pdb=" C2D NDP E3001 " pdb=" C4D NDP E3001 " pdb=" O3D NDP E3001 " both_signs ideal model delta sigma weight residual False -2.71 -2.22 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1D NDP F3001 " pdb=" C2D NDP F3001 " pdb=" N1N NDP F3001 " pdb=" O4D NDP F3001 " both_signs ideal model delta sigma weight residual False 2.60 2.20 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 2615 not shown) Planarity restraints: 2925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F1802 " -0.190 2.00e-02 2.50e+03 2.73e-01 7.43e+02 pdb=" C GLU F1802 " 0.447 2.00e-02 2.50e+03 pdb=" O GLU F1802 " -0.248 2.00e-02 2.50e+03 pdb=" N ALA F1805 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 976 " -0.060 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO F 977 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO F 977 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 977 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA F1328 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA F1328 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA F1328 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU F1329 " -0.010 2.00e-02 2.50e+03 ... (remaining 2922 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1662 2.74 - 3.28: 16095 3.28 - 3.82: 29598 3.82 - 4.36: 34876 4.36 - 4.90: 59121 Nonbonded interactions: 141352 Sorted by model distance: nonbonded pdb=" OH TYR E 891 " pdb=" OG1 THR E 923 " model vdw 2.204 2.440 nonbonded pdb=" O PRO F1649 " pdb=" OG SER F1653 " model vdw 2.207 2.440 nonbonded pdb=" NE2 HIS F1674 " pdb=" OG SER F1756 " model vdw 2.218 2.520 nonbonded pdb=" N GLU E2012 " pdb=" OE1 GLU E2012 " model vdw 2.229 2.520 nonbonded pdb=" O LYS E1995 " pdb=" OG1 THR E1999 " model vdw 2.235 2.440 ... (remaining 141347 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 individual isotropic 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: 0.760 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: 4.290 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 46.940 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.017 1.637 16630 Z= 1.078 Angle : 0.980 60.916 22718 Z= 0.526 Chirality : 0.050 0.534 2618 Planarity : 0.006 0.273 2925 Dihedral : 16.317 166.093 5744 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 2.06 % Allowed : 23.38 % Favored : 74.56 % 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: 0.27 (0.19), residues: 2154 helix: 0.84 (0.20), residues: 756 sheet: -0.45 (0.26), residues: 425 loop : 0.13 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F1442 HIS 0.004 0.001 HIS E1674 PHE 0.025 0.001 PHE E2109 TYR 0.022 0.001 TYR F 991 ARG 0.006 0.000 ARG E1545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: E 1010 GLU cc_start: 0.7973 (tt0) cc_final: 0.7742 (tt0) REVERT: F 1294 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7741 (mm-40) outliers start: 33 outliers final: 30 residues processed: 110 average time/residue: 1.0141 time to fit residues: 129.5735 Evaluate side-chains 106 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 930 THR Chi-restraints excluded: chain E residue 939 GLU Chi-restraints excluded: chain E residue 1000 ASP Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1480 THR Chi-restraints excluded: chain E residue 1584 SER Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1584 SER Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1836 VAL Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1915 THR Chi-restraints excluded: chain F residue 1991 VAL Chi-restraints excluded: chain F residue 2022 VAL Chi-restraints excluded: chain F residue 2024 CYS Chi-restraints excluded: chain F residue 2032 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16630 Z= 0.232 Angle : 0.523 11.795 22718 Z= 0.256 Chirality : 0.041 0.162 2618 Planarity : 0.003 0.038 2925 Dihedral : 7.314 156.538 2408 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.86 % Favored : 98.10 % Rotamer: Outliers : 2.68 % Allowed : 21.88 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 2156 helix: 0.93 (0.20), residues: 760 sheet: -0.55 (0.25), residues: 430 loop : 0.17 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1807 HIS 0.004 0.001 HIS E1674 PHE 0.011 0.001 PHE F1117 TYR 0.024 0.001 TYR E 991 ARG 0.005 0.000 ARG F1819 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 1.654 Fit side-chains REVERT: E 1010 GLU cc_start: 0.7954 (tt0) cc_final: 0.7705 (tt0) REVERT: E 1071 ASP cc_start: 0.8889 (m-30) cc_final: 0.8558 (t0) REVERT: E 1767 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8875 (mt) REVERT: E 1782 MET cc_start: 0.9026 (mtp) cc_final: 0.8796 (mtm) REVERT: F 1442 TRP cc_start: 0.7842 (m-90) cc_final: 0.7079 (m-90) outliers start: 43 outliers final: 19 residues processed: 117 average time/residue: 0.8485 time to fit residues: 117.1239 Evaluate side-chains 101 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1806 ASP Chi-restraints excluded: chain F residue 1865 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 213 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1848 HIS E1970 ASN F1940 GLN ** F2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16630 Z= 0.174 Angle : 0.492 10.313 22718 Z= 0.242 Chirality : 0.040 0.181 2618 Planarity : 0.003 0.036 2925 Dihedral : 6.667 149.615 2377 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.12 % Allowed : 21.76 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2156 helix: 1.06 (0.20), residues: 755 sheet: -0.47 (0.25), residues: 434 loop : 0.15 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.011 0.001 PHE F1117 TYR 0.020 0.001 TYR F 991 ARG 0.004 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 91 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: E 1010 GLU cc_start: 0.7940 (tt0) cc_final: 0.7728 (tt0) REVERT: E 1071 ASP cc_start: 0.8867 (m-30) cc_final: 0.8544 (t0) REVERT: E 1767 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8836 (mt) REVERT: E 1773 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: F 1294 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7792 (mm-40) REVERT: F 1768 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7714 (tp30) outliers start: 50 outliers final: 20 residues processed: 130 average time/residue: 0.9746 time to fit residues: 146.5624 Evaluate side-chains 109 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1980 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 103 optimal weight: 0.0370 chunk 187 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16630 Z= 0.273 Angle : 0.527 12.927 22718 Z= 0.259 Chirality : 0.042 0.199 2618 Planarity : 0.003 0.035 2925 Dihedral : 6.431 147.648 2375 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.81 % Allowed : 22.19 % Favored : 75.00 % 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: 0.31 (0.19), residues: 2156 helix: 0.96 (0.20), residues: 762 sheet: -0.61 (0.25), residues: 439 loop : 0.17 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.012 0.001 PHE E 944 TYR 0.026 0.001 TYR E 991 ARG 0.004 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 1.864 Fit side-chains REVERT: E 881 ASP cc_start: 0.8265 (t70) cc_final: 0.7957 (t70) REVERT: E 1071 ASP cc_start: 0.8825 (m-30) cc_final: 0.8495 (t0) REVERT: E 1767 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8873 (mt) REVERT: F 1294 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7804 (mm-40) REVERT: F 1768 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7833 (tp30) outliers start: 45 outliers final: 24 residues processed: 124 average time/residue: 0.9208 time to fit residues: 132.8800 Evaluate side-chains 110 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1474 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain E residue 2111 LEU Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1865 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 16630 Z= 0.285 Angle : 0.529 9.888 22718 Z= 0.261 Chirality : 0.042 0.192 2618 Planarity : 0.003 0.036 2925 Dihedral : 6.422 146.832 2375 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.68 % Allowed : 21.38 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 2156 helix: 0.95 (0.20), residues: 761 sheet: -0.60 (0.26), residues: 425 loop : 0.17 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F1442 HIS 0.003 0.001 HIS F1093 PHE 0.022 0.001 PHE E2109 TYR 0.024 0.002 TYR E 991 ARG 0.005 0.000 ARG F1439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 92 time to evaluate : 1.817 Fit side-chains REVERT: E 881 ASP cc_start: 0.8279 (t70) cc_final: 0.7895 (t70) REVERT: E 1071 ASP cc_start: 0.8829 (m-30) cc_final: 0.8522 (t0) REVERT: E 1671 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (tt) REVERT: E 1767 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8874 (mt) REVERT: E 1773 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: F 1294 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7820 (mm-40) REVERT: F 1442 TRP cc_start: 0.7377 (m-90) cc_final: 0.6334 (m-90) REVERT: F 1474 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (tm) REVERT: F 1768 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7907 (tp30) REVERT: F 1874 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8328 (t) outliers start: 59 outliers final: 29 residues processed: 138 average time/residue: 0.8512 time to fit residues: 138.1622 Evaluate side-chains 122 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 894 ILE Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1454 VAL Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1671 LEU Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain E residue 2111 LEU Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1413 ILE Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Chi-restraints excluded: chain F residue 1980 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16630 Z= 0.221 Angle : 0.517 13.049 22718 Z= 0.253 Chirality : 0.041 0.174 2618 Planarity : 0.003 0.036 2925 Dihedral : 6.228 143.371 2373 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.49 % Allowed : 21.70 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2156 helix: 1.03 (0.20), residues: 755 sheet: -0.62 (0.26), residues: 420 loop : 0.15 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.021 0.001 PHE E2109 TYR 0.023 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 92 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: E 881 ASP cc_start: 0.8206 (t70) cc_final: 0.7796 (t70) REVERT: E 1071 ASP cc_start: 0.8807 (m-30) cc_final: 0.8505 (t0) REVERT: E 1671 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8746 (tt) REVERT: E 1767 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8857 (mt) REVERT: E 1773 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8609 (m-30) REVERT: E 1835 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: F 1294 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: F 1442 TRP cc_start: 0.7440 (m-90) cc_final: 0.6530 (m-90) REVERT: F 1474 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8771 (tm) REVERT: F 1768 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7920 (tp30) REVERT: F 1874 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8325 (t) REVERT: F 2041 MET cc_start: 0.8908 (mtm) cc_final: 0.8661 (mtm) outliers start: 56 outliers final: 33 residues processed: 135 average time/residue: 0.9192 time to fit residues: 145.1607 Evaluate side-chains 126 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 86 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1454 VAL Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1671 LEU Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1835 GLN Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain E residue 2111 LEU Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1802 GLU Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 209 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 chunk 96 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 987 GLN F1110 GLN F1345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16630 Z= 0.273 Angle : 0.533 9.947 22718 Z= 0.262 Chirality : 0.041 0.181 2618 Planarity : 0.003 0.052 2925 Dihedral : 6.249 142.976 2373 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.49 % Allowed : 21.57 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 2156 helix: 0.99 (0.20), residues: 755 sheet: -0.69 (0.25), residues: 436 loop : 0.15 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.012 0.001 PHE E 944 TYR 0.025 0.002 TYR E 991 ARG 0.004 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 86 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: E 881 ASP cc_start: 0.8141 (t70) cc_final: 0.7696 (t70) REVERT: E 1071 ASP cc_start: 0.8811 (m-30) cc_final: 0.8508 (t0) REVERT: E 1538 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7985 (mmp80) REVERT: E 1671 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8773 (tt) REVERT: E 1767 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8870 (mt) REVERT: E 1773 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: F 1046 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8423 (mt) REVERT: F 1294 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: F 1442 TRP cc_start: 0.7506 (m-90) cc_final: 0.6724 (m-90) REVERT: F 1474 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8786 (tm) REVERT: F 1666 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7750 (mmp80) REVERT: F 1768 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: F 1874 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8353 (t) REVERT: F 2041 MET cc_start: 0.8920 (mtm) cc_final: 0.8709 (mtm) outliers start: 56 outliers final: 33 residues processed: 127 average time/residue: 0.9107 time to fit residues: 134.4001 Evaluate side-chains 128 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 85 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1036 MET Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1671 LEU Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2020 SER Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1768 GLU Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1802 GLU Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 124 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 164 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16630 Z= 0.218 Angle : 0.526 13.633 22718 Z= 0.256 Chirality : 0.041 0.188 2618 Planarity : 0.003 0.041 2925 Dihedral : 6.160 139.879 2373 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.62 % Allowed : 21.32 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 2156 helix: 1.03 (0.20), residues: 756 sheet: -0.67 (0.26), residues: 422 loop : 0.16 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.019 0.001 PHE E2109 TYR 0.022 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 85 time to evaluate : 1.441 Fit side-chains REVERT: E 881 ASP cc_start: 0.8122 (t70) cc_final: 0.7690 (t70) REVERT: E 1071 ASP cc_start: 0.8794 (m-30) cc_final: 0.8504 (t0) REVERT: E 1538 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7982 (mmp80) REVERT: E 1671 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8736 (tt) REVERT: E 1767 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8854 (mt) REVERT: E 1773 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: F 1294 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: F 1442 TRP cc_start: 0.7523 (m-90) cc_final: 0.6740 (m-90) REVERT: F 1462 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7767 (ptp-170) REVERT: F 1474 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8772 (tm) REVERT: F 1666 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7697 (mmp80) REVERT: F 1768 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7922 (tp30) REVERT: F 1874 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (t) outliers start: 58 outliers final: 34 residues processed: 132 average time/residue: 0.8930 time to fit residues: 137.5926 Evaluate side-chains 124 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 82 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1036 MET Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1538 ARG Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1671 LEU Chi-restraints excluded: chain E residue 1716 ASP Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1980 LEU Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2020 SER Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 947 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1071 ASP Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1597 SER Chi-restraints excluded: chain F residue 1666 ARG Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Chi-restraints excluded: chain F residue 1980 LEU Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 84 optimal weight: 0.1980 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 127 optimal weight: 50.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1848 HIS F1110 GLN F1970 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16630 Z= 0.170 Angle : 0.511 11.157 22718 Z= 0.249 Chirality : 0.040 0.200 2618 Planarity : 0.003 0.037 2925 Dihedral : 5.947 131.006 2373 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.56 % Allowed : 22.38 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2156 helix: 1.11 (0.20), residues: 754 sheet: -0.65 (0.26), residues: 422 loop : 0.18 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1807 HIS 0.004 0.001 HIS F1093 PHE 0.019 0.001 PHE E2109 TYR 0.019 0.001 TYR F 991 ARG 0.005 0.000 ARG F1462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 88 time to evaluate : 1.748 Fit side-chains REVERT: E 881 ASP cc_start: 0.8090 (t70) cc_final: 0.7655 (t70) REVERT: E 1010 GLU cc_start: 0.7908 (tt0) cc_final: 0.7587 (tt0) REVERT: E 1767 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8832 (mt) REVERT: E 1773 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8614 (m-30) REVERT: F 1294 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: F 1442 TRP cc_start: 0.7523 (m-90) cc_final: 0.6858 (m-90) REVERT: F 1462 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7673 (ptp-170) REVERT: F 1474 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8754 (tm) REVERT: F 1768 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7956 (tp30) REVERT: F 1874 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8339 (t) outliers start: 41 outliers final: 25 residues processed: 119 average time/residue: 1.0032 time to fit residues: 139.5824 Evaluate side-chains 113 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2020 SER Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1801 ASN Chi-restraints excluded: chain F residue 1852 VAL Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.9980 chunk 125 optimal weight: 50.0000 chunk 97 optimal weight: 4.9990 chunk 143 optimal weight: 50.0000 chunk 216 optimal weight: 0.0270 chunk 198 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 136 optimal weight: 8.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E2086 GLN F1110 GLN F1970 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16630 Z= 0.174 Angle : 0.524 12.886 22718 Z= 0.255 Chirality : 0.041 0.205 2618 Planarity : 0.003 0.036 2925 Dihedral : 5.883 126.661 2371 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.12 % Allowed : 22.94 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2156 helix: 1.14 (0.20), residues: 754 sheet: -0.64 (0.26), residues: 422 loop : 0.20 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.020 0.001 PHE E2109 TYR 0.020 0.001 TYR F 991 ARG 0.005 0.000 ARG F1462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 1.824 Fit side-chains REVERT: E 881 ASP cc_start: 0.8093 (t70) cc_final: 0.7659 (t70) REVERT: E 1010 GLU cc_start: 0.7902 (tt0) cc_final: 0.7592 (tt0) REVERT: E 1767 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8837 (mt) REVERT: E 1773 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8611 (m-30) REVERT: F 1294 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7815 (mm-40) REVERT: F 1442 TRP cc_start: 0.7522 (m-90) cc_final: 0.6964 (m-90) REVERT: F 1462 ARG cc_start: 0.8079 (ptp90) cc_final: 0.7637 (ptp-170) REVERT: F 1474 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8762 (tm) REVERT: F 1768 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7956 (tp30) REVERT: F 1874 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (t) outliers start: 34 outliers final: 24 residues processed: 110 average time/residue: 0.9318 time to fit residues: 119.8289 Evaluate side-chains 107 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 1443 LEU Chi-restraints excluded: chain E residue 1627 LEU Chi-restraints excluded: chain E residue 1651 VAL Chi-restraints excluded: chain E residue 1726 THR Chi-restraints excluded: chain E residue 1727 SER Chi-restraints excluded: chain E residue 1767 LEU Chi-restraints excluded: chain E residue 1773 ASP Chi-restraints excluded: chain E residue 1941 VAL Chi-restraints excluded: chain E residue 1984 THR Chi-restraints excluded: chain E residue 1991 VAL Chi-restraints excluded: chain E residue 2020 SER Chi-restraints excluded: chain E residue 2068 ILE Chi-restraints excluded: chain F residue 867 SER Chi-restraints excluded: chain F residue 976 THR Chi-restraints excluded: chain F residue 1046 LEU Chi-restraints excluded: chain F residue 1086 VAL Chi-restraints excluded: chain F residue 1111 VAL Chi-restraints excluded: chain F residue 1113 ILE Chi-restraints excluded: chain F residue 1115 GLU Chi-restraints excluded: chain F residue 1294 GLN Chi-restraints excluded: chain F residue 1441 VAL Chi-restraints excluded: chain F residue 1474 LEU Chi-restraints excluded: chain F residue 1518 LEU Chi-restraints excluded: chain F residue 1537 THR Chi-restraints excluded: chain F residue 1790 THR Chi-restraints excluded: chain F residue 1865 LEU Chi-restraints excluded: chain F residue 1874 SER Chi-restraints excluded: chain F residue 2022 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 151 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.120906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079940 restraints weight = 26777.400| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.61 r_work: 0.3035 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16630 Z= 0.184 Angle : 0.517 11.345 22718 Z= 0.252 Chirality : 0.041 0.214 2618 Planarity : 0.003 0.037 2925 Dihedral : 5.837 121.769 2371 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.18 % Allowed : 23.19 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2156 helix: 1.17 (0.20), residues: 754 sheet: -0.65 (0.26), residues: 419 loop : 0.23 (0.21), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1807 HIS 0.003 0.001 HIS F1093 PHE 0.020 0.001 PHE E2109 TYR 0.021 0.001 TYR E 991 ARG 0.005 0.000 ARG F1462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.06 seconds wall clock time: 79 minutes 37.90 seconds (4777.90 seconds total)