Starting phenix.real_space_refine on Tue May 13 16:12:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy2_43644/05_2025/8vy2_43644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy2_43644/05_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_43644/05_2025/8vy2_43644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy2_43644/05_2025/8vy2_43644.map" model { file = "/net/cci-nas-00/data/ceres_data/8vy2_43644/05_2025/8vy2_43644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy2_43644/05_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-5687/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: 6.51, per 1000 atoms: 0.63 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 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: 1.79 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: 5.61 Time building geometry restraints manager: 3.10 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.990 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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 : 1.130 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: 0.2758 time to fit residues: 109.4644 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 : 1.137 ------------------------------------------------------------------------------- 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 = 0.155419 restraints weight = 33168.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154800 restraints weight = 35752.164| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 1.066 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: 0.8805 (tt) cc_final: 0.8439 (tp) REVERT: A 1307 THR cc_start: 0.8482 (m) cc_final: 0.8218 (m) REVERT: A 1811 MET cc_start: 0.8288 (mpp) cc_final: 0.7942 (mpp) REVERT: A 1815 TYR cc_start: 0.8572 (m-80) cc_final: 0.8233 (m-80) REVERT: A 1833 MET cc_start: -0.2682 (mmt) cc_final: -0.3471 (mmm) REVERT: A 2195 GLU cc_start: 0.6601 (tp30) cc_final: 0.6381 (tt0) REVERT: A 2268 PHE cc_start: 0.6431 (m-10) cc_final: 0.6158 (m-10) REVERT: A 2457 THR cc_start: 0.7823 (m) cc_final: 0.7497 (p) outliers start: 5 outliers final: 0 residues processed: 179 average time/residue: 0.2226 time to fit residues: 56.0129 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 : 1.065 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1329 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.154641 restraints weight = 21951.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.152913 restraints weight = 36706.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152396 restraints weight = 38106.876| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10662 Z= 0.157 Angle : 0.735 12.004 14536 Z= 0.368 Chirality : 0.047 0.275 1630 Planarity : 0.004 0.051 1894 Dihedral : 7.356 58.511 1742 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 0.26 % Allowed : 4.14 % Favored : 95.59 % 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: -0.86 (0.24), residues: 1315 helix: 0.53 (0.43), residues: 153 sheet: -0.19 (0.30), residues: 289 loop : -0.93 (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 0.017 0.002 TYR A2250 ARG 0.019 0.001 ARG A2136 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 10) link_NAG-ASN : angle 3.74095 ( 30) link_BETA1-4 : bond 0.00535 ( 5) link_BETA1-4 : angle 2.23448 ( 15) hydrogen bonds : bond 0.04291 ( 352) hydrogen bonds : angle 6.03366 ( 972) SS BOND : bond 0.01125 ( 36) SS BOND : angle 2.57659 ( 72) covalent geometry : bond 0.00347 (10611) covalent geometry : angle 0.69086 (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 : 1.055 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: 0.8774 (tt) cc_final: 0.8428 (tp) REVERT: A 1795 GLU cc_start: 0.6273 (tt0) cc_final: 0.6034 (pt0) REVERT: A 1833 MET cc_start: -0.2944 (mmt) cc_final: -0.4900 (mmm) REVERT: A 2457 THR cc_start: 0.7873 (m) cc_final: 0.7551 (p) outliers start: 3 outliers final: 1 residues processed: 151 average time/residue: 0.2161 time to fit residues: 47.0587 Evaluate side-chains 102 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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: 10.0000 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4007 r_free = 0.4007 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146323 restraints weight = 21667.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145240 restraints weight = 42566.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144837 restraints weight = 42113.203| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10662 Z= 0.206 Angle : 0.753 8.042 14536 Z= 0.385 Chirality : 0.047 0.193 1630 Planarity : 0.005 0.061 1894 Dihedral : 6.764 58.997 1742 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % 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: -1.01 (0.23), residues: 1315 helix: 0.51 (0.42), residues: 156 sheet: -0.26 (0.29), residues: 303 loop : -1.09 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1906 HIS 0.007 0.001 HIS A1791 PHE 0.013 0.002 PHE A1462 TYR 0.048 0.003 TYR A1815 ARG 0.004 0.001 ARG A2046 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 10) link_NAG-ASN : angle 2.58000 ( 30) link_BETA1-4 : bond 0.00525 ( 5) link_BETA1-4 : angle 2.05715 ( 15) hydrogen bonds : bond 0.05060 ( 352) hydrogen bonds : angle 6.02432 ( 972) SS BOND : bond 0.00763 ( 36) SS BOND : angle 2.21951 ( 72) covalent geometry : bond 0.00481 (10611) covalent geometry : angle 0.72671 (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 142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.032 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: A 1833 MET cc_start: -0.3466 (mmt) cc_final: -0.4643 (mmm) REVERT: A 2395 TYR cc_start: 0.6979 (t80) cc_final: 0.6580 (t80) REVERT: A 2457 THR cc_start: 0.7943 (m) cc_final: 0.7625 (p) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.2090 time to fit residues: 42.6031 Evaluate side-chains 96 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 0.0270 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1274 ASN A1562 HIS ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.160099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149639 restraints weight = 21249.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147090 restraints weight = 40375.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146194 restraints weight = 40096.562| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10662 Z= 0.156 Angle : 0.688 10.462 14536 Z= 0.352 Chirality : 0.046 0.210 1630 Planarity : 0.005 0.078 1894 Dihedral : 6.500 58.679 1742 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -0.91 (0.23), residues: 1315 helix: 0.66 (0.41), residues: 156 sheet: -0.06 (0.31), residues: 282 loop : -1.07 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1906 HIS 0.008 0.001 HIS A1791 PHE 0.017 0.002 PHE A2428 TYR 0.032 0.002 TYR A1815 ARG 0.007 0.001 ARG A1849 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 10) link_NAG-ASN : angle 2.27461 ( 30) link_BETA1-4 : bond 0.00458 ( 5) link_BETA1-4 : angle 1.76050 ( 15) hydrogen bonds : bond 0.04399 ( 352) hydrogen bonds : angle 5.68637 ( 972) SS BOND : bond 0.00873 ( 36) SS BOND : angle 2.37272 ( 72) covalent geometry : bond 0.00355 (10611) covalent geometry : angle 0.65951 (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 132 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.101 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: 0.7677 (m-30) cc_final: 0.7173 (t0) REVERT: A 1795 GLU cc_start: 0.6315 (tt0) cc_final: 0.5899 (pt0) REVERT: A 2195 GLU cc_start: 0.7409 (tt0) cc_final: 0.7206 (tt0) REVERT: A 2395 TYR cc_start: 0.7032 (t80) cc_final: 0.6596 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2307 time to fit residues: 42.9768 Evaluate side-chains 85 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 95 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2369 HIS ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145557 restraints weight = 21552.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143508 restraints weight = 42952.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142291 restraints weight = 36154.701| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10662 Z= 0.210 Angle : 0.769 11.442 14536 Z= 0.395 Chirality : 0.048 0.207 1630 Planarity : 0.005 0.052 1894 Dihedral : 6.620 58.373 1742 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -1.14 (0.23), residues: 1315 helix: 0.46 (0.40), residues: 158 sheet: -0.29 (0.29), residues: 296 loop : -1.20 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A2111 HIS 0.008 0.001 HIS A1791 PHE 0.018 0.002 PHE A1462 TYR 0.032 0.002 TYR A1815 ARG 0.009 0.001 ARG A2028 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 10) link_NAG-ASN : angle 2.92917 ( 30) link_BETA1-4 : bond 0.00383 ( 5) link_BETA1-4 : angle 1.83573 ( 15) hydrogen bonds : bond 0.05378 ( 352) hydrogen bonds : angle 5.89451 ( 972) SS BOND : bond 0.00702 ( 36) SS BOND : angle 2.53054 ( 72) covalent geometry : bond 0.00497 (10611) covalent geometry : angle 0.73697 (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 127 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.096 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: 0.7739 (m-30) cc_final: 0.7133 (t70) REVERT: A 1307 THR cc_start: 0.8655 (m) cc_final: 0.8237 (p) REVERT: A 1795 GLU cc_start: 0.6171 (tt0) cc_final: 0.5742 (pt0) REVERT: A 1833 MET cc_start: -0.2985 (mmt) cc_final: -0.3243 (tpp) REVERT: A 2361 THR cc_start: 0.8292 (p) cc_final: 0.7778 (p) REVERT: A 2395 TYR cc_start: 0.7077 (t80) cc_final: 0.6219 (t80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2300 time to fit residues: 41.1964 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 : 1.054 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2036 GLN A2369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145503 restraints weight = 21667.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.143792 restraints weight = 41660.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142991 restraints weight = 37192.886| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10662 Z= 0.167 Angle : 0.716 13.688 14536 Z= 0.366 Chirality : 0.047 0.223 1630 Planarity : 0.004 0.047 1894 Dihedral : 6.481 58.286 1742 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: -1.02 (0.23), residues: 1315 helix: 0.64 (0.41), residues: 158 sheet: -0.15 (0.30), residues: 296 loop : -1.16 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A2111 HIS 0.006 0.001 HIS A2199 PHE 0.026 0.002 PHE A2021 TYR 0.017 0.002 TYR A2250 ARG 0.015 0.001 ARG A1797 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 2.31721 ( 30) link_BETA1-4 : bond 0.00506 ( 5) link_BETA1-4 : angle 1.68381 ( 15) hydrogen bonds : bond 0.04700 ( 352) hydrogen bonds : angle 5.67475 ( 972) SS BOND : bond 0.00914 ( 36) SS BOND : angle 2.54856 ( 72) covalent geometry : bond 0.00385 (10611) covalent geometry : angle 0.68525 (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 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.155 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: 0.7712 (m-30) cc_final: 0.7074 (t70) REVERT: A 1307 THR cc_start: 0.8604 (m) cc_final: 0.8218 (p) REVERT: A 1815 TYR cc_start: 0.8617 (m-80) cc_final: 0.8239 (m-80) REVERT: A 2244 ARG cc_start: 0.7396 (tpp80) cc_final: 0.7094 (tpp80) REVERT: A 2395 TYR cc_start: 0.7138 (t80) cc_final: 0.6891 (t80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2226 time to fit residues: 37.9016 Evaluate side-chains 75 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS A2455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141480 restraints weight = 21010.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139410 restraints weight = 42972.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.137720 restraints weight = 29419.449| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10662 Z= 0.148 Angle : 0.712 17.877 14536 Z= 0.364 Chirality : 0.046 0.204 1630 Planarity : 0.005 0.116 1894 Dihedral : 6.332 59.486 1742 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -0.98 (0.23), residues: 1315 helix: 0.71 (0.41), residues: 158 sheet: -0.11 (0.29), residues: 309 loop : -1.17 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2111 HIS 0.005 0.001 HIS A1755 PHE 0.022 0.001 PHE A1290 TYR 0.014 0.001 TYR A2370 ARG 0.006 0.000 ARG A2184 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.13262 ( 30) link_BETA1-4 : bond 0.00454 ( 5) link_BETA1-4 : angle 1.54857 ( 15) hydrogen bonds : bond 0.04304 ( 352) hydrogen bonds : angle 5.44291 ( 972) SS BOND : bond 0.01013 ( 36) SS BOND : angle 3.00140 ( 72) covalent geometry : bond 0.00340 (10611) covalent geometry : angle 0.67441 (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 120 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.043 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: 0.7863 (m-30) cc_final: 0.7163 (t70) REVERT: A 1307 THR cc_start: 0.8608 (m) cc_final: 0.8170 (p) REVERT: A 1833 MET cc_start: -0.4068 (mmp) cc_final: -0.6310 (ppp) REVERT: A 2395 TYR cc_start: 0.7300 (t80) cc_final: 0.7060 (t80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2123 time to fit residues: 37.0798 Evaluate side-chains 74 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 6.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 0.1980 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1684 ASN ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2455 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138733 restraints weight = 21405.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.138371 restraints weight = 41514.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139082 restraints weight = 36132.079| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10662 Z= 0.128 Angle : 0.673 14.636 14536 Z= 0.345 Chirality : 0.046 0.212 1630 Planarity : 0.005 0.099 1894 Dihedral : 6.182 59.776 1742 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 : 0.24 % 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: -0.87 (0.23), residues: 1315 helix: 0.73 (0.40), residues: 159 sheet: 0.07 (0.31), residues: 295 loop : -1.11 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1789 HIS 0.009 0.001 HIS A1584 PHE 0.023 0.001 PHE A1290 TYR 0.013 0.001 TYR A2359 ARG 0.009 0.000 ARG A2360 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 10) link_NAG-ASN : angle 2.01924 ( 30) link_BETA1-4 : bond 0.00477 ( 5) link_BETA1-4 : angle 1.49112 ( 15) hydrogen bonds : bond 0.03981 ( 352) hydrogen bonds : angle 5.34576 ( 972) SS BOND : bond 0.00702 ( 36) SS BOND : angle 2.51293 ( 72) covalent geometry : bond 0.00287 (10611) covalent geometry : angle 0.64389 (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 117 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.134 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: 0.7845 (m-30) cc_final: 0.7116 (t70) REVERT: A 1307 THR cc_start: 0.8597 (m) cc_final: 0.8164 (p) REVERT: A 1833 MET cc_start: -0.3847 (mmp) cc_final: -0.6116 (ppp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.2309 time to fit residues: 38.7377 Evaluate side-chains 77 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.154976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143963 restraints weight = 21588.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142103 restraints weight = 43101.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140662 restraints weight = 36658.857| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10662 Z= 0.195 Angle : 0.759 21.955 14536 Z= 0.390 Chirality : 0.048 0.236 1630 Planarity : 0.005 0.093 1894 Dihedral : 6.416 57.937 1742 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -1.09 (0.23), residues: 1315 helix: 0.47 (0.40), residues: 158 sheet: -0.22 (0.30), residues: 302 loop : -1.18 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A1789 HIS 0.007 0.001 HIS A2199 PHE 0.018 0.002 PHE A1462 TYR 0.017 0.002 TYR A2250 ARG 0.004 0.001 ARG A2184 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 10) link_NAG-ASN : angle 2.24195 ( 30) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 1.65510 ( 15) hydrogen bonds : bond 0.05026 ( 352) hydrogen bonds : angle 5.53542 ( 972) SS BOND : bond 0.00919 ( 36) SS BOND : angle 3.45940 ( 72) covalent geometry : bond 0.00457 (10611) covalent geometry : angle 0.71201 (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 115 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1180 ASP cc_start: 0.7954 (m-30) cc_final: 0.7293 (t0) REVERT: A 1307 THR cc_start: 0.8697 (m) cc_final: 0.8309 (p) REVERT: A 1815 TYR cc_start: 0.8596 (m-80) cc_final: 0.8207 (m-80) REVERT: A 1833 MET cc_start: -0.3370 (mmp) cc_final: -0.5904 (ppp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2202 time to fit residues: 36.6644 Evaluate side-chains 74 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142564 restraints weight = 21346.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.141082 restraints weight = 41224.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139356 restraints weight = 32607.882| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10662 Z= 0.160 Angle : 0.695 13.966 14536 Z= 0.358 Chirality : 0.046 0.190 1630 Planarity : 0.005 0.088 1894 Dihedral : 6.378 58.102 1742 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 : 0.24 % 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: -1.05 (0.23), residues: 1315 helix: 0.53 (0.40), residues: 158 sheet: -0.36 (0.29), residues: 312 loop : -1.10 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1789 HIS 0.005 0.001 HIS A1755 PHE 0.028 0.002 PHE A2273 TYR 0.018 0.002 TYR A2250 ARG 0.007 0.000 ARG A2169 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 10) link_NAG-ASN : angle 2.11558 ( 30) link_BETA1-4 : bond 0.00440 ( 5) link_BETA1-4 : angle 1.56047 ( 15) hydrogen bonds : bond 0.04608 ( 352) hydrogen bonds : angle 5.44856 ( 972) SS BOND : bond 0.00786 ( 36) SS BOND : angle 2.43341 ( 72) covalent geometry : bond 0.00374 (10611) covalent geometry : angle 0.66765 (14419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.83 seconds wall clock time: 53 minutes 28.13 seconds (3208.13 seconds total)