Starting phenix.real_space_refine on Mon Jul 28 21:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.map" model { file = "/net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy2_43644/07_2025/8vy2_43644.cif" } resolution = 4.3 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 6463 2.51 5 N 1813 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10167 Classifications: {'peptide': 1319} Link IDs: {'PCIS': 5, 'PTRANS': 76, 'TRANS': 1237} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.52, per 1000 atoms: 0.72 Number of scatterers: 10374 At special positions: 0 Unit cell: (83.6, 126.5, 159.5, 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 89 16.00 O 2009 8.00 N 1813 7.00 C 6463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A1322 " - pdb=" SG CYS A1333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1327 " - pdb=" SG CYS A1364 " distance=2.03 Simple disulfide: pdb=" SG CYS A1366 " - pdb=" SG CYS A1375 " distance=2.03 Simple disulfide: pdb=" SG CYS A1382 " - pdb=" SG CYS A1393 " distance=2.03 Simple disulfide: pdb=" SG CYS A1387 " - pdb=" SG CYS A1402 " distance=2.03 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1404 " distance=2.03 Simple disulfide: pdb=" SG CYS A1404 " - pdb=" SG CYS A1413 " distance=2.02 Simple disulfide: pdb=" SG CYS A1422 " - pdb=" SG CYS A1433 " distance=2.03 Simple disulfide: pdb=" SG CYS A1427 " - pdb=" SG CYS A1443 " distance=2.03 Simple disulfide: pdb=" SG CYS A1445 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1577 " - pdb=" SG CYS A1594 " distance=2.03 Simple disulfide: pdb=" SG CYS A1635 " - pdb=" SG CYS A1661 " distance=2.04 Simple disulfide: pdb=" SG CYS A1668 " - pdb=" SG CYS A1679 " distance=2.03 Simple disulfide: pdb=" SG CYS A1673 " - pdb=" SG CYS A1688 " distance=2.03 Simple disulfide: pdb=" SG CYS A1690 " - pdb=" SG CYS A1699 " distance=2.03 Simple disulfide: pdb=" SG CYS A1855 " - pdb=" SG CYS A1885 " distance=2.03 Simple disulfide: pdb=" SG CYS A1891 " - pdb=" SG CYS A1902 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1911 " distance=2.04 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1913 " distance=2.90 Simple disulfide: pdb=" SG CYS A1911 " - pdb=" SG CYS A1913 " distance=2.05 Simple disulfide: pdb=" SG CYS A1913 " - pdb=" SG CYS A1922 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1937 " distance=2.03 Simple disulfide: pdb=" SG CYS A1931 " - pdb=" SG CYS A1949 " distance=2.03 Simple disulfide: pdb=" SG CYS A1951 " - pdb=" SG CYS A1960 " distance=2.03 Simple disulfide: pdb=" SG CYS A1968 " - pdb=" SG CYS A1978 " distance=2.03 Simple disulfide: pdb=" SG CYS A1981 " - pdb=" SG CYS A1993 " distance=2.04 Simple disulfide: pdb=" SG CYS A1983 " - pdb=" SG CYS A2000 " distance=2.03 Simple disulfide: pdb=" SG CYS A2002 " - pdb=" SG CYS A2015 " distance=2.03 Simple disulfide: pdb=" SG CYS A2018 " - pdb=" SG CYS A2030 " distance=2.03 Simple disulfide: pdb=" SG CYS A2020 " - pdb=" SG CYS A2037 " distance=2.03 Simple disulfide: pdb=" SG CYS A2039 " - pdb=" SG CYS A2048 " distance=2.03 Simple disulfide: pdb=" SG CYS A2051 " - pdb=" SG CYS A2063 " distance=2.03 Simple disulfide: pdb=" SG CYS A2070 " - pdb=" SG CYS A2105 " distance=2.03 Simple disulfide: pdb=" SG CYS A2093 " - pdb=" SG CYS A2119 " distance=2.03 Simple disulfide: pdb=" SG CYS A2426 " - pdb=" SG CYS A2458 " distance=2.04 Simple disulfide: pdb=" SG CYS A2446 " - pdb=" SG CYS A2460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2501 " - " ASN A1591 " " NAG A2502 " - " ASN A1994 " " NAG A2503 " - " ASN A2137 " " NAG A2504 " - " ASN A2155 " " NAG A2505 " - " ASN A2160 " " NAG A2506 " - " ASN A1264 " " NAG B 1 " - " ASN A1154 " " NAG C 1 " - " ASN A1302 " " NAG D 1 " - " ASN A1638 " " NAG E 1 " - " ASN A1655 " Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 27 sheets defined 17.7% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 1179 through 1182 Processing helix chain 'A' and resid 1214 through 1220 Processing helix chain 'A' and resid 1238 through 1251 removed outlier: 3.834A pdb=" N ALA A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1291 through 1302 removed outlier: 3.952A pdb=" N ASN A1302 " --> pdb=" O GLN A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1311 Processing helix chain 'A' and resid 1320 through 1325 removed outlier: 3.567A pdb=" N LEU A1323 " --> pdb=" O ASN A1320 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A1324 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 removed outlier: 3.570A pdb=" N SER A1384 " --> pdb=" O LEU A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1391 removed outlier: 3.678A pdb=" N ASN A1390 " --> pdb=" O CYS A1387 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A1391 " --> pdb=" O GLY A1388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1387 through 1391' Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 6.835A pdb=" N SER A1587 " --> pdb=" O VAL A1583 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR A1588 " --> pdb=" O HIS A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1665 Processing helix chain 'A' and resid 1759 through 1762 Processing helix chain 'A' and resid 1889 through 1893 removed outlier: 3.572A pdb=" N SER A1893 " --> pdb=" O PRO A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1929 Processing helix chain 'A' and resid 1984 through 1987 Processing helix chain 'A' and resid 2074 through 2078 Processing helix chain 'A' and resid 2124 through 2135 removed outlier: 3.750A pdb=" N LYS A2133 " --> pdb=" O ALA A2129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A2134 " --> pdb=" O LEU A2130 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A2135 " --> pdb=" O ASN A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2142 through 2158 Processing helix chain 'A' and resid 2164 through 2185 removed outlier: 3.576A pdb=" N GLN A2185 " --> pdb=" O HIS A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2194 removed outlier: 3.616A pdb=" N LEU A2190 " --> pdb=" O GLY A2187 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA A2191 " --> pdb=" O PHE A2188 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA A2192 " --> pdb=" O ASP A2189 " (cutoff:3.500A) Processing helix chain 'A' and resid 2197 through 2210 Processing helix chain 'A' and resid 2211 through 2213 No H-bonds generated for 'chain 'A' and resid 2211 through 2213' Processing helix chain 'A' and resid 2214 through 2222 removed outlier: 3.872A pdb=" N GLN A2220 " --> pdb=" O ALA A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2250 removed outlier: 4.888A pdb=" N LYS A2247 " --> pdb=" O ALA A2243 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG A2248 " --> pdb=" O ARG A2244 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2273 No H-bonds generated for 'chain 'A' and resid 2271 through 2273' Processing helix chain 'A' and resid 2289 through 2293 Processing helix chain 'A' and resid 2361 through 2366 Processing sheet with id=AA1, first strand: chain 'A' and resid 1154 through 1157 removed outlier: 3.956A pdb=" N LEU A1352 " --> pdb=" O GLN A1120 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1122 " --> pdb=" O LEU A1352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1140 through 1141 removed outlier: 4.124A pdb=" N GLY A1140 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1222 through 1227 removed outlier: 3.870A pdb=" N VAL A1275 " --> pdb=" O VAL A1224 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1226 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A1274 " --> pdb=" O GLN A1263 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A1263 " --> pdb=" O ASN A1274 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A1278 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL A1259 " --> pdb=" O SER A1278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1332 through 1342 removed outlier: 6.938A pdb=" N HIS A1357 " --> pdb=" O ASP A1340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1370 through 1371 Processing sheet with id=AA6, first strand: chain 'A' and resid 1393 through 1396 Processing sheet with id=AA7, first strand: chain 'A' and resid 1408 through 1409 Processing sheet with id=AA8, first strand: chain 'A' and resid 1432 through 1435 Processing sheet with id=AA9, first strand: chain 'A' and resid 1595 through 1601 removed outlier: 4.498A pdb=" N ASN A1554 " --> pdb=" O HIS A1562 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS A1552 " --> pdb=" O PRO A1564 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N GLY A1566 " --> pdb=" O TYR A1550 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N TYR A1550 " --> pdb=" O GLY A1566 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N LYS A1568 " --> pdb=" O GLN A1548 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N GLN A1548 " --> pdb=" O LYS A1568 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N ALA A1570 " --> pdb=" O LEU A1546 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N LEU A1546 " --> pdb=" O ALA A1570 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N VAL A1572 " --> pdb=" O SER A1544 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N SER A1544 " --> pdb=" O VAL A1572 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR A1480 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE A1641 " --> pdb=" O THR A1480 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER A1482 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A1639 " --> pdb=" O SER A1482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1595 through 1601 removed outlier: 4.498A pdb=" N ASN A1554 " --> pdb=" O HIS A1562 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS A1552 " --> pdb=" O PRO A1564 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N GLY A1566 " --> pdb=" O TYR A1550 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N TYR A1550 " --> pdb=" O GLY A1566 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N LYS A1568 " --> pdb=" O GLN A1548 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N GLN A1548 " --> pdb=" O LYS A1568 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N ALA A1570 " --> pdb=" O LEU A1546 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N LEU A1546 " --> pdb=" O ALA A1570 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N VAL A1572 " --> pdb=" O SER A1544 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N SER A1544 " --> pdb=" O VAL A1572 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR A1480 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE A1641 " --> pdb=" O THR A1480 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER A1482 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A1639 " --> pdb=" O SER A1482 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A1658 " --> pdb=" O SER A1461 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1526 through 1529 removed outlier: 6.035A pdb=" N ILE A1511 " --> pdb=" O LEU A1493 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A1493 " --> pdb=" O ILE A1511 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A1496 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A1614 " --> pdb=" O TYR A1496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1678 through 1682 Processing sheet with id=AB4, first strand: chain 'A' and resid 1818 through 1824 removed outlier: 3.504A pdb=" N TYR A1807 " --> pdb=" O ILE A1824 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR A1729 " --> pdb=" O MET A1861 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET A1861 " --> pdb=" O TYR A1729 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A1731 " --> pdb=" O VAL A1859 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A1859 " --> pdb=" O GLY A1731 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET A1733 " --> pdb=" O GLN A1857 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A1708 " --> pdb=" O LYS A1882 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS A1882 " --> pdb=" O ARG A1708 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1715 through 1717 removed outlier: 3.580A pdb=" N ILE A1836 " --> pdb=" O TRP A1717 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1902 through 1904 removed outlier: 3.950A pdb=" N ARG A1903 " --> pdb=" O SER A1910 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A1910 " --> pdb=" O ARG A1903 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1936 through 1938 Processing sheet with id=AB8, first strand: chain 'A' and resid 1955 through 1956 Processing sheet with id=AB9, first strand: chain 'A' and resid 1972 through 1973 Processing sheet with id=AC1, first strand: chain 'A' and resid 1989 through 1993 removed outlier: 4.444A pdb=" N GLN A2001 " --> pdb=" O ASP A1990 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2006 through 2007 Processing sheet with id=AC3, first strand: chain 'A' and resid 2043 through 2044 Processing sheet with id=AC4, first strand: chain 'A' and resid 2056 through 2059 Processing sheet with id=AC5, first strand: chain 'A' and resid 2088 through 2091 Processing sheet with id=AC6, first strand: chain 'A' and resid 2097 through 2098 Processing sheet with id=AC7, first strand: chain 'A' and resid 2254 through 2258 removed outlier: 3.605A pdb=" N VAL A2384 " --> pdb=" O MET A2470 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2254 through 2258 removed outlier: 4.994A pdb=" N SER A2465 " --> pdb=" O TRP A2429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2276 through 2278 removed outlier: 6.702A pdb=" N GLN A2459 " --> pdb=" O LEU A2448 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A2448 " --> pdb=" O GLN A2459 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1823 1.32 - 1.46: 3285 1.46 - 1.59: 5393 1.59 - 1.72: 0 1.72 - 1.86: 110 Bond restraints: 10611 Sorted by residual: bond pdb=" N ASN A1261 " pdb=" CA ASN A1261 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.25e-02 6.40e+03 1.42e+01 bond pdb=" C PRO A1117 " pdb=" O PRO A1117 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" N ILE A1262 " pdb=" CA ILE A1262 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N THR A1835 " pdb=" CA THR A1835 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" N ILE A1272 " pdb=" CA ILE A1272 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.18e-02 7.18e+03 1.08e+01 ... (remaining 10606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 13785 2.14 - 4.28: 568 4.28 - 6.42: 54 6.42 - 8.56: 8 8.56 - 10.70: 4 Bond angle restraints: 14419 Sorted by residual: angle pdb=" C PRO A2081 " pdb=" N GLN A2082 " pdb=" CA GLN A2082 " ideal model delta sigma weight residual 120.87 110.17 10.70 1.42e+00 4.96e-01 5.67e+01 angle pdb=" C ASP A1118 " pdb=" N PHE A1119 " pdb=" CA PHE A1119 " ideal model delta sigma weight residual 122.36 112.12 10.24 1.60e+00 3.91e-01 4.09e+01 angle pdb=" C PRO A2081 " pdb=" CA PRO A2081 " pdb=" CB PRO A2081 " ideal model delta sigma weight residual 111.56 101.56 10.00 1.65e+00 3.67e-01 3.67e+01 angle pdb=" C PRO A1114 " pdb=" CA PRO A1114 " pdb=" CB PRO A1114 " ideal model delta sigma weight residual 111.56 102.10 9.46 1.65e+00 3.67e-01 3.29e+01 angle pdb=" N PRO A1237 " pdb=" CA PRO A1237 " pdb=" CB PRO A1237 " ideal model delta sigma weight residual 103.25 97.41 5.84 1.05e+00 9.07e-01 3.09e+01 ... (remaining 14414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 6239 21.23 - 42.46: 340 42.46 - 63.68: 61 63.68 - 84.91: 18 84.91 - 106.14: 4 Dihedral angle restraints: 6662 sinusoidal: 2887 harmonic: 3775 Sorted by residual: dihedral pdb=" CB CYS A1855 " pdb=" SG CYS A1855 " pdb=" SG CYS A1885 " pdb=" CB CYS A1885 " ideal model delta sinusoidal sigma weight residual -86.00 -159.22 73.22 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS A1327 " pdb=" SG CYS A1327 " pdb=" SG CYS A1364 " pdb=" CB CYS A1364 " ideal model delta sinusoidal sigma weight residual 93.00 163.66 -70.66 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS A1387 " pdb=" SG CYS A1387 " pdb=" SG CYS A1402 " pdb=" CB CYS A1402 " ideal model delta sinusoidal sigma weight residual 93.00 154.11 -61.11 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 6659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1561 0.116 - 0.233: 59 0.233 - 0.349: 7 0.349 - 0.465: 2 0.465 - 0.581: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.59e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.95e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.38e+01 ... (remaining 1627 not shown) Planarity restraints: 1904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG D 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2502 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG A2502 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A2502 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A2502 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A2502 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2501 " -0.346 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A2501 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A2501 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG A2501 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG A2501 " -0.104 2.00e-02 2.50e+03 ... (remaining 1901 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1182 2.75 - 3.29: 10384 3.29 - 3.82: 16866 3.82 - 4.36: 19094 4.36 - 4.90: 31655 Nonbonded interactions: 79181 Sorted by model distance: nonbonded pdb=" OG1 THR A2059 " pdb=" OE1 GLU A2064 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A1310 " pdb=" OE1 GLN A1312 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A1762 " pdb=" NH1 ARG A1783 " model vdw 2.226 3.120 nonbonded pdb=" OG1 THR A1736 " pdb=" O ARG A1853 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A2240 " pdb=" NH1 ARG A2244 " model vdw 2.236 3.120 ... (remaining 79176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 33.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 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 : 0.010 0.868 10662 Z= 0.547 Angle : 1.033 46.131 14536 Z= 0.626 Chirality : 0.058 0.581 1630 Planarity : 0.020 0.305 1894 Dihedral : 13.164 106.137 4130 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.60 % Favored : 91.94 % Rotamer: Outliers : 0.97 % Allowed : 1.85 % Favored : 97.18 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 6.17 % 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: -0.91 (0.23), residues: 1315 helix: 0.79 (0.44), residues: 138 sheet: -0.65 (0.30), residues: 298 loop : -0.82 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1906 HIS 0.008 0.001 HIS A2234 PHE 0.028 0.002 PHE A1353 TYR 0.018 0.002 TYR A1592 ARG 0.006 0.001 ARG A2233 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 10) link_NAG-ASN : angle 2.68540 ( 30) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 2.20658 ( 15) hydrogen bonds : bond 0.15805 ( 352) hydrogen bonds : angle 7.51017 ( 972) SS BOND : bond 0.14480 ( 36) SS BOND : angle 6.81117 ( 72) covalent geometry : bond 0.00546 (10611) covalent geometry : angle 0.90735 (14419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1373 ASP cc_start: 0.8058 (m-30) cc_final: 0.7847 (t0) REVERT: A 1604 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7568 (mmmt) REVERT: A 1610 THR cc_start: 0.4963 (p) cc_final: 0.4513 (p) REVERT: A 1618 VAL cc_start: 0.8156 (m) cc_final: 0.7845 (p) REVERT: A 1759 LEU cc_start: 0.7597 (tp) cc_final: 0.7158 (tt) REVERT: A 1811 MET cc_start: 0.6556 (mpp) cc_final: 0.6347 (mpp) REVERT: A 1871 LEU cc_start: 0.7407 (mt) cc_final: 0.7110 (mt) REVERT: A 1882 LYS cc_start: 0.8088 (tptt) cc_final: 0.7654 (mmtt) REVERT: A 2270 LYS cc_start: 0.5718 (mttt) cc_final: 0.3977 (mttm) REVERT: A 2301 ASP cc_start: 0.9234 (m-30) cc_final: 0.8912 (p0) REVERT: A 2457 THR cc_start: 0.7254 (m) cc_final: 0.6847 (p) outliers start: 11 outliers final: 2 residues processed: 301 average time/residue: 0.2874 time to fit residues: 114.9497 Evaluate side-chains 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 33 optimal weight: 0.0040 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.0272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 GLN A1329 ASN A1357 HIS A1412 HIS A1478 HIS A1491 ASN A1557 HIS A1674 GLN ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 ASN A2104 HIS A2118 ASN A2199 HIS A2230 GLN A2241 ASN ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2455 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.168040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157174 restraints weight = 21393.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155420 restraints weight = 33167.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154500 restraints weight = 35731.239| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10662 Z= 0.195 Angle : 0.899 28.307 14536 Z= 0.445 Chirality : 0.049 0.197 1630 Planarity : 0.006 0.073 1894 Dihedral : 8.584 65.012 1742 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.46 % Favored : 93.31 % Rotamer: Outliers : 0.44 % Allowed : 4.93 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.89 (0.23), residues: 1315 helix: 0.54 (0.42), residues: 152 sheet: -0.30 (0.29), residues: 298 loop : -0.92 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2441 HIS 0.007 0.001 HIS A2369 PHE 0.039 0.002 PHE A2021 TYR 0.017 0.002 TYR A1762 ARG 0.008 0.001 ARG A2136 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 10) link_NAG-ASN : angle 2.98166 ( 30) link_BETA1-4 : bond 0.00503 ( 5) link_BETA1-4 : angle 2.43882 ( 15) hydrogen bonds : bond 0.04934 ( 352) hydrogen bonds : angle 6.37641 ( 972) SS BOND : bond 0.01148 ( 36) SS BOND : angle 5.83329 ( 72) covalent geometry : bond 0.00435 (10611) covalent geometry : angle 0.78788 (14419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1167 LEU cc_start: 0.8788 (tt) cc_final: 0.8423 (tp) REVERT: A 1307 THR cc_start: 0.8455 (m) cc_final: 0.8192 (m) REVERT: A 1811 MET cc_start: 0.8287 (mpp) cc_final: 0.7944 (mpp) REVERT: A 1815 TYR cc_start: 0.8564 (m-80) cc_final: 0.8226 (m-80) REVERT: A 1833 MET cc_start: -0.2667 (mmt) cc_final: -0.3462 (mmm) REVERT: A 2195 GLU cc_start: 0.6603 (tp30) cc_final: 0.6402 (tt0) REVERT: A 2268 PHE cc_start: 0.6416 (m-10) cc_final: 0.6146 (m-10) REVERT: A 2457 THR cc_start: 0.7806 (m) cc_final: 0.7486 (p) outliers start: 5 outliers final: 0 residues processed: 179 average time/residue: 0.2256 time to fit residues: 56.7618 Evaluate side-chains 111 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1357 HIS A1429 ASN A1562 HIS ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1819 GLN A1826 ASN ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156288 restraints weight = 21961.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154871 restraints weight = 34122.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154027 restraints weight = 37971.128| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10662 Z= 0.157 Angle : 0.736 11.973 14536 Z= 0.368 Chirality : 0.046 0.273 1630 Planarity : 0.004 0.051 1894 Dihedral : 7.349 58.211 1742 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.69 % Rotamer: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.85 (0.24), residues: 1315 helix: 0.55 (0.43), residues: 153 sheet: -0.19 (0.30), residues: 289 loop : -0.92 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1789 HIS 0.005 0.001 HIS A1755 PHE 0.024 0.002 PHE A2021 TYR 0.016 0.002 TYR A2250 ARG 0.018 0.001 ARG A2136 Details of bonding type rmsd link_NAG-ASN : bond 0.00886 ( 10) link_NAG-ASN : angle 3.69317 ( 30) link_BETA1-4 : bond 0.00424 ( 5) link_BETA1-4 : angle 2.24399 ( 15) hydrogen bonds : bond 0.04215 ( 352) hydrogen bonds : angle 6.01797 ( 972) SS BOND : bond 0.01013 ( 36) SS BOND : angle 2.65617 ( 72) covalent geometry : bond 0.00347 (10611) covalent geometry : angle 0.69128 (14419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1167 LEU cc_start: 0.8770 (tt) cc_final: 0.8425 (tp) REVERT: A 1795 GLU cc_start: 0.6241 (tt0) cc_final: 0.6011 (pt0) REVERT: A 1833 MET cc_start: -0.2919 (mmt) cc_final: -0.4898 (mmm) REVERT: A 2457 THR cc_start: 0.7860 (m) cc_final: 0.7544 (p) outliers start: 3 outliers final: 1 residues processed: 151 average time/residue: 0.2118 time to fit residues: 46.2681 Evaluate side-chains 105 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1329 ASN A1357 HIS A1551 ASN A1857 GLN ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145908 restraints weight = 20981.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145061 restraints weight = 40553.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.144617 restraints weight = 29308.773| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10662 Z= 0.169 Angle : 0.718 8.349 14536 Z= 0.366 Chirality : 0.047 0.188 1630 Planarity : 0.004 0.038 1894 Dihedral : 6.662 58.542 1742 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.92 (0.23), residues: 1315 helix: 0.63 (0.43), residues: 156 sheet: -0.13 (0.30), residues: 291 loop : -1.05 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1906 HIS 0.006 0.001 HIS A2181 PHE 0.014 0.002 PHE A1694 TYR 0.044 0.002 TYR A1815 ARG 0.004 0.000 ARG A2244 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 10) link_NAG-ASN : angle 2.49098 ( 30) link_BETA1-4 : bond 0.00626 ( 5) link_BETA1-4 : angle 1.99632 ( 15) hydrogen bonds : bond 0.04638 ( 352) hydrogen bonds : angle 5.92601 ( 972) SS BOND : bond 0.00782 ( 36) SS BOND : angle 2.21723 ( 72) covalent geometry : bond 0.00386 (10611) covalent geometry : angle 0.69130 (14419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1167 LEU cc_start: 0.8864 (tt) cc_final: 0.8471 (tp) REVERT: A 1703 MET cc_start: 0.7871 (mmt) cc_final: 0.7503 (mpp) REVERT: A 1795 GLU cc_start: 0.6493 (tt0) cc_final: 0.6289 (pt0) REVERT: A 1833 MET cc_start: -0.3490 (mmt) cc_final: -0.4874 (mmm) REVERT: A 2195 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7696 (tt0) REVERT: A 2261 MET cc_start: 0.8596 (mmm) cc_final: 0.8276 (tpp) REVERT: A 2395 TYR cc_start: 0.7048 (t80) cc_final: 0.6306 (t80) REVERT: A 2457 THR cc_start: 0.8008 (m) cc_final: 0.7669 (p) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2574 time to fit residues: 52.0635 Evaluate side-chains 99 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 129 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 96 optimal weight: 0.0370 chunk 31 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS A2277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149278 restraints weight = 21249.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146792 restraints weight = 40303.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144906 restraints weight = 39472.818| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10662 Z= 0.166 Angle : 0.688 8.542 14536 Z= 0.352 Chirality : 0.046 0.173 1630 Planarity : 0.004 0.070 1894 Dihedral : 6.419 58.857 1742 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 0.18 % Allowed : 3.17 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1315 helix: 0.58 (0.41), residues: 156 sheet: -0.05 (0.31), residues: 282 loop : -1.07 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1789 HIS 0.012 0.001 HIS A1850 PHE 0.013 0.002 PHE A2188 TYR 0.016 0.002 TYR A2250 ARG 0.016 0.001 ARG A1849 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 10) link_NAG-ASN : angle 2.24675 ( 30) link_BETA1-4 : bond 0.00419 ( 5) link_BETA1-4 : angle 1.73125 ( 15) hydrogen bonds : bond 0.04456 ( 352) hydrogen bonds : angle 5.67830 ( 972) SS BOND : bond 0.00923 ( 36) SS BOND : angle 2.13437 ( 72) covalent geometry : bond 0.00379 (10611) covalent geometry : angle 0.66442 (14419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7682 (m-30) cc_final: 0.7178 (t70) REVERT: A 1636 MET cc_start: 0.8121 (mtp) cc_final: 0.7894 (mtm) REVERT: A 1733 MET cc_start: 0.6625 (ptm) cc_final: 0.5876 (ptp) REVERT: A 1833 MET cc_start: -0.3684 (mmt) cc_final: -0.5028 (mmm) REVERT: A 2195 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7840 (tt0) REVERT: A 2395 TYR cc_start: 0.6886 (t80) cc_final: 0.6528 (t80) REVERT: A 2428 PHE cc_start: 0.6633 (p90) cc_final: 0.6364 (p90) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.2221 time to fit residues: 44.5721 Evaluate side-chains 88 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 0.0030 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1274 ASN A2036 GLN A2369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148941 restraints weight = 21528.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147549 restraints weight = 38571.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145915 restraints weight = 35538.178| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10662 Z= 0.154 Angle : 0.693 8.905 14536 Z= 0.356 Chirality : 0.046 0.183 1630 Planarity : 0.005 0.103 1894 Dihedral : 6.413 58.753 1742 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.89 (0.23), residues: 1315 helix: 0.74 (0.41), residues: 156 sheet: -0.20 (0.31), residues: 293 loop : -1.01 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A2111 HIS 0.013 0.001 HIS A1755 PHE 0.019 0.002 PHE A2021 TYR 0.014 0.001 TYR A1330 ARG 0.008 0.001 ARG A2028 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 10) link_NAG-ASN : angle 2.72362 ( 30) link_BETA1-4 : bond 0.00469 ( 5) link_BETA1-4 : angle 1.69094 ( 15) hydrogen bonds : bond 0.04389 ( 352) hydrogen bonds : angle 5.57170 ( 972) SS BOND : bond 0.00638 ( 36) SS BOND : angle 2.25006 ( 72) covalent geometry : bond 0.00357 (10611) covalent geometry : angle 0.66386 (14419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7697 (m-30) cc_final: 0.7134 (t70) REVERT: A 1636 MET cc_start: 0.8030 (mtp) cc_final: 0.7817 (mtm) REVERT: A 1833 MET cc_start: -0.3652 (mmt) cc_final: -0.3974 (tpp) REVERT: A 2395 TYR cc_start: 0.7026 (t80) cc_final: 0.6298 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2279 time to fit residues: 41.6193 Evaluate side-chains 86 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1760 ASN A1791 HIS A2369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146456 restraints weight = 21674.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144312 restraints weight = 41061.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141609 restraints weight = 39191.347| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10662 Z= 0.184 Angle : 0.712 11.755 14536 Z= 0.367 Chirality : 0.046 0.178 1630 Planarity : 0.005 0.081 1894 Dihedral : 6.409 58.170 1742 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.94 (0.23), residues: 1315 helix: 0.63 (0.40), residues: 158 sheet: -0.21 (0.31), residues: 294 loop : -1.04 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A2111 HIS 0.012 0.001 HIS A1755 PHE 0.017 0.002 PHE A2428 TYR 0.016 0.002 TYR A2250 ARG 0.009 0.001 ARG A1394 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 10) link_NAG-ASN : angle 2.44232 ( 30) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 1.71498 ( 15) hydrogen bonds : bond 0.04779 ( 352) hydrogen bonds : angle 5.60164 ( 972) SS BOND : bond 0.00683 ( 36) SS BOND : angle 2.53560 ( 72) covalent geometry : bond 0.00432 (10611) covalent geometry : angle 0.68103 (14419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7695 (m-30) cc_final: 0.7100 (t70) REVERT: A 1307 THR cc_start: 0.8574 (m) cc_final: 0.8164 (p) REVERT: A 2395 TYR cc_start: 0.7074 (t80) cc_final: 0.6628 (t80) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2189 time to fit residues: 37.6041 Evaluate side-chains 85 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 101 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 0.0020 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2245 ASN A2369 HIS A2455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143465 restraints weight = 21084.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140893 restraints weight = 39815.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138618 restraints weight = 30290.546| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10662 Z= 0.136 Angle : 0.678 15.430 14536 Z= 0.346 Chirality : 0.045 0.178 1630 Planarity : 0.004 0.069 1894 Dihedral : 6.251 59.267 1742 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.81 (0.23), residues: 1315 helix: 0.77 (0.41), residues: 158 sheet: -0.02 (0.31), residues: 293 loop : -1.02 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2111 HIS 0.010 0.001 HIS A1755 PHE 0.023 0.002 PHE A2021 TYR 0.018 0.001 TYR A1330 ARG 0.008 0.001 ARG A1394 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 10) link_NAG-ASN : angle 2.13688 ( 30) link_BETA1-4 : bond 0.00476 ( 5) link_BETA1-4 : angle 1.53508 ( 15) hydrogen bonds : bond 0.04105 ( 352) hydrogen bonds : angle 5.39629 ( 972) SS BOND : bond 0.00681 ( 36) SS BOND : angle 2.67810 ( 72) covalent geometry : bond 0.00310 (10611) covalent geometry : angle 0.64502 (14419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7899 (m-30) cc_final: 0.7148 (t70) REVERT: A 1307 THR cc_start: 0.8545 (m) cc_final: 0.8142 (p) REVERT: A 1833 MET cc_start: -0.3209 (mmt) cc_final: -0.4254 (tpp) REVERT: A 2395 TYR cc_start: 0.7207 (t80) cc_final: 0.6834 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2205 time to fit residues: 39.1717 Evaluate side-chains 78 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 118 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 90 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1760 ASN A2245 ASN A2455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147153 restraints weight = 21751.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146119 restraints weight = 40483.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144751 restraints weight = 30466.806| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10662 Z= 0.123 Angle : 0.671 22.059 14536 Z= 0.343 Chirality : 0.045 0.218 1630 Planarity : 0.004 0.059 1894 Dihedral : 6.069 59.036 1742 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.78 (0.23), residues: 1315 helix: 0.80 (0.40), residues: 159 sheet: 0.01 (0.30), residues: 311 loop : -1.01 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2111 HIS 0.010 0.001 HIS A1755 PHE 0.017 0.001 PHE A2021 TYR 0.018 0.001 TYR A2250 ARG 0.006 0.000 ARG A1392 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 10) link_NAG-ASN : angle 1.95199 ( 30) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 1.46269 ( 15) hydrogen bonds : bond 0.03656 ( 352) hydrogen bonds : angle 5.28396 ( 972) SS BOND : bond 0.00845 ( 36) SS BOND : angle 3.36496 ( 72) covalent geometry : bond 0.00266 (10611) covalent geometry : angle 0.62270 (14419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7785 (m-30) cc_final: 0.7056 (t70) REVERT: A 1307 THR cc_start: 0.8468 (m) cc_final: 0.8062 (p) REVERT: A 1833 MET cc_start: -0.3324 (mmt) cc_final: -0.4442 (tpp) REVERT: A 2244 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6980 (tpp80) REVERT: A 2266 ASP cc_start: 0.8925 (p0) cc_final: 0.7979 (m-30) REVERT: A 2395 TYR cc_start: 0.7300 (t80) cc_final: 0.6731 (t80) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.2311 time to fit residues: 41.2451 Evaluate side-chains 84 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1857 GLN A2131 ASN A2455 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138911 restraints weight = 21758.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136984 restraints weight = 46442.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135405 restraints weight = 39210.816| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.7060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 10662 Z= 0.326 Angle : 0.954 19.661 14536 Z= 0.488 Chirality : 0.054 0.295 1630 Planarity : 0.006 0.057 1894 Dihedral : 6.967 59.890 1742 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.42 (0.22), residues: 1315 helix: -0.12 (0.38), residues: 158 sheet: -0.50 (0.29), residues: 312 loop : -1.32 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1728 HIS 0.014 0.002 HIS A2199 PHE 0.039 0.003 PHE A1462 TYR 0.023 0.003 TYR A2359 ARG 0.007 0.001 ARG A1637 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 10) link_NAG-ASN : angle 2.83951 ( 30) link_BETA1-4 : bond 0.00258 ( 5) link_BETA1-4 : angle 2.07533 ( 15) hydrogen bonds : bond 0.07081 ( 352) hydrogen bonds : angle 6.26487 ( 972) SS BOND : bond 0.00990 ( 36) SS BOND : angle 3.74545 ( 72) covalent geometry : bond 0.00789 (10611) covalent geometry : angle 0.90886 (14419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1307 THR cc_start: 0.8872 (m) cc_final: 0.8522 (p) REVERT: A 1833 MET cc_start: -0.3303 (mmt) cc_final: -0.4211 (tpp) REVERT: A 2219 GLU cc_start: 0.7066 (tp30) cc_final: 0.6832 (tm-30) REVERT: A 2361 THR cc_start: 0.8701 (p) cc_final: 0.8331 (p) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2652 time to fit residues: 44.5266 Evaluate side-chains 71 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142184 restraints weight = 21315.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139906 restraints weight = 44770.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138705 restraints weight = 39687.579| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10662 Z= 0.188 Angle : 0.771 20.250 14536 Z= 0.396 Chirality : 0.047 0.200 1630 Planarity : 0.005 0.062 1894 Dihedral : 6.641 58.749 1742 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.29 (0.23), residues: 1315 helix: 0.16 (0.38), residues: 158 sheet: -0.39 (0.29), residues: 312 loop : -1.29 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2111 HIS 0.011 0.001 HIS A1755 PHE 0.018 0.002 PHE A1290 TYR 0.017 0.002 TYR A2359 ARG 0.008 0.001 ARG A2169 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 10) link_NAG-ASN : angle 2.29372 ( 30) link_BETA1-4 : bond 0.00414 ( 5) link_BETA1-4 : angle 1.66686 ( 15) hydrogen bonds : bond 0.05273 ( 352) hydrogen bonds : angle 5.71318 ( 972) SS BOND : bond 0.00785 ( 36) SS BOND : angle 3.65435 ( 72) covalent geometry : bond 0.00449 (10611) covalent geometry : angle 0.71980 (14419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.18 seconds wall clock time: 56 minutes 36.92 seconds (3396.92 seconds total)