Starting phenix.real_space_refine on Sat Aug 23 07:59:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy2_43644/08_2025/8vy2_43644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy2_43644/08_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_43644/08_2025/8vy2_43644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy2_43644/08_2025/8vy2_43644.map" model { file = "/net/cci-nas-00/data/ceres_data/8vy2_43644/08_2025/8vy2_43644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy2_43644/08_2025/8vy2_43644.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.48, per 1000 atoms: 0.24 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: 1.09 Conformation dependent library (CDL) restraints added in 430.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.59 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: 2.59 Time building geometry restraints manager: 1.32 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- 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 : 13.17 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (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 ARG 0.006 0.001 ARG A2233 TYR 0.018 0.002 TYR A1592 PHE 0.028 0.002 PHE A1353 TRP 0.011 0.002 TRP A1906 HIS 0.008 0.001 HIS A2234 Details of bonding type rmsd covalent geometry : bond 0.00546 (10611) covalent geometry : angle 0.90735 (14419) SS BOND : bond 0.14480 ( 36) SS BOND : angle 6.81117 ( 72) hydrogen bonds : bond 0.15805 ( 352) hydrogen bonds : angle 7.51017 ( 972) link_BETA1-4 : bond 0.00348 ( 5) link_BETA1-4 : angle 2.20658 ( 15) link_NAG-ASN : bond 0.00568 ( 10) link_NAG-ASN : angle 2.68540 ( 30) *********************** 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 : 0.377 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: 0.7846 (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: 0.6348 (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: 0.7655 (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: 0.1195 time to fit residues: 47.3674 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1120 GLN A1231 GLN A1329 ASN A1412 HIS A1478 HIS A1491 ASN A1554 ASN A1557 HIS A1674 GLN ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1819 GLN A1826 ASN A2104 HIS A2118 ASN A2199 HIS ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.160204 restraints weight = 21725.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157547 restraints weight = 32978.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.156534 restraints weight = 37077.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.156080 restraints weight = 34272.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156018 restraints weight = 32630.081| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10662 Z= 0.175 Angle : 0.884 27.389 14536 Z= 0.436 Chirality : 0.049 0.267 1630 Planarity : 0.006 0.075 1894 Dihedral : 8.715 66.899 1742 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.54 % Rotamer: Outliers : 0.44 % Allowed : 5.11 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.23), residues: 1315 helix: 0.63 (0.42), residues: 152 sheet: -0.21 (0.30), residues: 294 loop : -0.88 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1735 TYR 0.017 0.002 TYR A1762 PHE 0.041 0.002 PHE A2021 TRP 0.024 0.002 TRP A2441 HIS 0.006 0.001 HIS A1982 Details of bonding type rmsd covalent geometry : bond 0.00391 (10611) covalent geometry : angle 0.77066 (14419) SS BOND : bond 0.01324 ( 36) SS BOND : angle 5.79823 ( 72) hydrogen bonds : bond 0.04605 ( 352) hydrogen bonds : angle 6.33619 ( 972) link_BETA1-4 : bond 0.00711 ( 5) link_BETA1-4 : angle 2.53682 ( 15) link_NAG-ASN : bond 0.00751 ( 10) link_NAG-ASN : angle 3.07566 ( 30) *********************** 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 180 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 175 time to evaluate : 0.388 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: symmetry clash revert: symmetry clash REVERT: A 1167 LEU cc_start: 0.8768 (tt) cc_final: 0.8395 (tp) REVERT: A 1307 THR cc_start: 0.8358 (m) cc_final: 0.8012 (m) REVERT: A 1811 MET cc_start: 0.8193 (mpp) cc_final: 0.7906 (mpp) REVERT: A 1815 TYR cc_start: 0.8520 (m-80) cc_final: 0.8284 (m-80) REVERT: A 1833 MET cc_start: -0.2516 (mmt) cc_final: -0.3394 (mmm) REVERT: A 2268 PHE cc_start: 0.6399 (m-10) cc_final: 0.6108 (m-10) REVERT: A 2457 THR cc_start: 0.7833 (m) cc_final: 0.7538 (p) outliers start: 5 outliers final: 0 residues processed: 177 average time/residue: 0.0929 time to fit residues: 23.4714 Evaluate side-chains 114 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 95 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 GLN ** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1551 ASN A1562 HIS A1826 ASN A2023 HIS ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2230 GLN A2241 ASN ** A2277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.155036 restraints weight = 22043.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153763 restraints weight = 33326.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152483 restraints weight = 37317.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151756 restraints weight = 36435.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150659 restraints weight = 37458.975| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10662 Z= 0.179 Angle : 0.767 16.848 14536 Z= 0.384 Chirality : 0.048 0.296 1630 Planarity : 0.005 0.048 1894 Dihedral : 7.357 58.180 1742 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.39 % Favored : 93.46 % Rotamer: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.24), residues: 1315 helix: 0.37 (0.42), residues: 153 sheet: -0.25 (0.29), residues: 301 loop : -0.97 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG A2136 TYR 0.018 0.002 TYR A2250 PHE 0.028 0.002 PHE A2021 TRP 0.016 0.001 TRP A1789 HIS 0.005 0.001 HIS A2181 Details of bonding type rmsd covalent geometry : bond 0.00403 (10611) covalent geometry : angle 0.71915 (14419) SS BOND : bond 0.01076 ( 36) SS BOND : angle 2.54119 ( 72) hydrogen bonds : bond 0.04568 ( 352) hydrogen bonds : angle 6.07568 ( 972) link_BETA1-4 : bond 0.00336 ( 5) link_BETA1-4 : angle 2.55479 ( 15) link_NAG-ASN : bond 0.01087 ( 10) link_NAG-ASN : angle 4.24711 ( 30) *********************** 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 153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.370 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: A 1167 LEU cc_start: 0.8806 (tt) cc_final: 0.8473 (tp) REVERT: A 1307 THR cc_start: 0.8327 (m) cc_final: 0.8063 (m) REVERT: A 1330 TYR cc_start: 0.7350 (m-80) cc_final: 0.7064 (m-80) REVERT: A 1811 MET cc_start: 0.8215 (mpp) cc_final: 0.7980 (mpp) REVERT: A 1833 MET cc_start: -0.3023 (mmt) cc_final: -0.4697 (mmm) REVERT: A 2395 TYR cc_start: 0.6672 (t80) cc_final: 0.6072 (t80) REVERT: A 2457 THR cc_start: 0.7884 (m) cc_final: 0.7446 (p) outliers start: 2 outliers final: 1 residues processed: 152 average time/residue: 0.0828 time to fit residues: 18.0494 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1312 GLN A1429 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150963 restraints weight = 21734.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.150600 restraints weight = 39377.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150510 restraints weight = 35316.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149770 restraints weight = 30015.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149745 restraints weight = 27259.829| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10662 Z= 0.145 Angle : 0.670 7.870 14536 Z= 0.341 Chirality : 0.045 0.172 1630 Planarity : 0.004 0.064 1894 Dihedral : 6.667 58.352 1742 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 0.18 % Allowed : 2.82 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.23), residues: 1315 helix: 0.53 (0.43), residues: 156 sheet: -0.13 (0.31), residues: 277 loop : -0.97 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2050 TYR 0.042 0.002 TYR A1815 PHE 0.018 0.001 PHE A2021 TRP 0.009 0.001 TRP A1789 HIS 0.007 0.001 HIS A1791 Details of bonding type rmsd covalent geometry : bond 0.00318 (10611) covalent geometry : angle 0.64652 (14419) SS BOND : bond 0.01022 ( 36) SS BOND : angle 1.89482 ( 72) hydrogen bonds : bond 0.04081 ( 352) hydrogen bonds : angle 5.80063 ( 972) link_BETA1-4 : bond 0.00547 ( 5) link_BETA1-4 : angle 1.87957 ( 15) link_NAG-ASN : bond 0.00947 ( 10) link_NAG-ASN : angle 2.44575 ( 30) *********************** 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 133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.319 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: A 1167 LEU cc_start: 0.8886 (tt) cc_final: 0.8521 (tp) REVERT: A 1307 THR cc_start: 0.8331 (m) cc_final: 0.8117 (m) REVERT: A 1330 TYR cc_start: 0.7431 (m-80) cc_final: 0.7070 (m-80) REVERT: A 1811 MET cc_start: 0.8044 (mpp) cc_final: 0.6919 (mpp) REVERT: A 1833 MET cc_start: -0.3260 (mmt) cc_final: -0.4824 (mmm) REVERT: A 2395 TYR cc_start: 0.6857 (t80) cc_final: 0.6092 (t80) REVERT: A 2457 THR cc_start: 0.7882 (m) cc_final: 0.7491 (p) outliers start: 2 outliers final: 0 residues processed: 132 average time/residue: 0.0830 time to fit residues: 15.8510 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 : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 63 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS ** A2277 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 = 0.4054 r_free = 0.4054 target = 0.163779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.153601 restraints weight = 21584.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.152018 restraints weight = 34715.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150809 restraints weight = 38555.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150628 restraints weight = 37552.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150672 restraints weight = 32138.584| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10662 Z= 0.135 Angle : 0.661 8.473 14536 Z= 0.338 Chirality : 0.045 0.190 1630 Planarity : 0.004 0.050 1894 Dihedral : 6.295 59.872 1742 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.24), residues: 1315 helix: 0.73 (0.42), residues: 156 sheet: -0.08 (0.30), residues: 296 loop : -0.98 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2140 TYR 0.030 0.002 TYR A1815 PHE 0.019 0.001 PHE A2428 TRP 0.010 0.001 TRP A1906 HIS 0.006 0.001 HIS A1791 Details of bonding type rmsd covalent geometry : bond 0.00303 (10611) covalent geometry : angle 0.63721 (14419) SS BOND : bond 0.00831 ( 36) SS BOND : angle 2.12913 ( 72) hydrogen bonds : bond 0.03873 ( 352) hydrogen bonds : angle 5.52455 ( 972) link_BETA1-4 : bond 0.00493 ( 5) link_BETA1-4 : angle 1.69274 ( 15) link_NAG-ASN : bond 0.00345 ( 10) link_NAG-ASN : angle 2.09237 ( 30) *********************** 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 138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.443 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: A 1180 ASP cc_start: 0.7539 (m-30) cc_final: 0.7188 (t70) REVERT: A 1811 MET cc_start: 0.8012 (mpp) cc_final: 0.6927 (mpp) REVERT: A 1833 MET cc_start: -0.3553 (mmt) cc_final: -0.4889 (mmm) REVERT: A 2395 TYR cc_start: 0.6980 (t80) cc_final: 0.6015 (t80) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.0892 time to fit residues: 17.6655 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 0.0060 chunk 57 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS A1584 HIS A1684 ASN A2036 GLN A2245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153288 restraints weight = 21791.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151843 restraints weight = 39743.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151468 restraints weight = 41042.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150024 restraints weight = 41677.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150256 restraints weight = 38243.914| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10662 Z= 0.122 Angle : 0.647 8.776 14536 Z= 0.330 Chirality : 0.044 0.173 1630 Planarity : 0.005 0.103 1894 Dihedral : 6.211 59.420 1742 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.18 % Allowed : 1.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1315 helix: 0.89 (0.42), residues: 156 sheet: -0.02 (0.30), residues: 296 loop : -0.99 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2103 TYR 0.030 0.001 TYR A1815 PHE 0.025 0.001 PHE A2021 TRP 0.039 0.002 TRP A2111 HIS 0.011 0.001 HIS A1850 Details of bonding type rmsd covalent geometry : bond 0.00260 (10611) covalent geometry : angle 0.61881 (14419) SS BOND : bond 0.00890 ( 36) SS BOND : angle 2.09925 ( 72) hydrogen bonds : bond 0.03581 ( 352) hydrogen bonds : angle 5.31630 ( 972) link_BETA1-4 : bond 0.00430 ( 5) link_BETA1-4 : angle 1.52787 ( 15) link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 2.64605 ( 30) *********************** 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 139 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.384 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: A 1167 LEU cc_start: 0.8775 (tt) cc_final: 0.8332 (tp) REVERT: A 1180 ASP cc_start: 0.7582 (m-30) cc_final: 0.7193 (t70) REVERT: A 1228 ASN cc_start: 0.7422 (p0) cc_final: 0.7173 (p0) REVERT: A 1815 TYR cc_start: 0.8594 (m-10) cc_final: 0.8392 (m-80) REVERT: A 1833 MET cc_start: -0.3701 (mmt) cc_final: -0.5218 (mmm) REVERT: A 2395 TYR cc_start: 0.7271 (t80) cc_final: 0.6616 (t80) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.0991 time to fit residues: 19.5804 Evaluate side-chains 101 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS A1584 HIS A1791 HIS A2245 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.162498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148776 restraints weight = 21437.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147879 restraints weight = 42503.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147183 restraints weight = 33928.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146344 restraints weight = 32544.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146534 restraints weight = 28583.190| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5627 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= 0.132 Angle : 0.648 11.293 14536 Z= 0.330 Chirality : 0.045 0.310 1630 Planarity : 0.004 0.079 1894 Dihedral : 6.062 59.659 1742 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1315 helix: 0.89 (0.42), residues: 158 sheet: 0.03 (0.30), residues: 298 loop : -0.96 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1392 TYR 0.026 0.002 TYR A1815 PHE 0.021 0.001 PHE A2428 TRP 0.026 0.001 TRP A2111 HIS 0.007 0.001 HIS A1791 Details of bonding type rmsd covalent geometry : bond 0.00292 (10611) covalent geometry : angle 0.62370 (14419) SS BOND : bond 0.00801 ( 36) SS BOND : angle 2.11366 ( 72) hydrogen bonds : bond 0.03747 ( 352) hydrogen bonds : angle 5.17725 ( 972) link_BETA1-4 : bond 0.00473 ( 5) link_BETA1-4 : angle 1.52946 ( 15) link_NAG-ASN : bond 0.00280 ( 10) link_NAG-ASN : angle 2.15748 ( 30) *********************** 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 131 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.259 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: A 1180 ASP cc_start: 0.7847 (m-30) cc_final: 0.7215 (t70) REVERT: A 1229 MET cc_start: 0.9185 (ttp) cc_final: 0.8964 (mtt) REVERT: A 1636 MET cc_start: 0.8046 (mtp) cc_final: 0.7803 (mtm) REVERT: A 1703 MET cc_start: 0.7916 (mmt) cc_final: 0.7597 (mpp) REVERT: A 1833 MET cc_start: -0.4104 (mmt) cc_final: -0.5505 (mmm) REVERT: A 2244 ARG cc_start: 0.7503 (tpp80) cc_final: 0.7200 (tpp80) REVERT: A 2395 TYR cc_start: 0.7202 (t80) cc_final: 0.6693 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0930 time to fit residues: 17.9030 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 : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 0.0040 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS A1584 HIS ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144893 restraints weight = 21062.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144195 restraints weight = 41370.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144699 restraints weight = 36048.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144998 restraints weight = 25413.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145112 restraints weight = 25370.088| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10662 Z= 0.126 Angle : 0.648 16.434 14536 Z= 0.329 Chirality : 0.045 0.264 1630 Planarity : 0.004 0.060 1894 Dihedral : 5.959 59.617 1742 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.23), residues: 1315 helix: 0.89 (0.42), residues: 159 sheet: 0.05 (0.30), residues: 298 loop : -0.97 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1394 TYR 0.016 0.001 TYR A2370 PHE 0.016 0.001 PHE A2413 TRP 0.020 0.001 TRP A2111 HIS 0.006 0.001 HIS A1791 Details of bonding type rmsd covalent geometry : bond 0.00278 (10611) covalent geometry : angle 0.61629 (14419) SS BOND : bond 0.00684 ( 36) SS BOND : angle 2.57339 ( 72) hydrogen bonds : bond 0.03631 ( 352) hydrogen bonds : angle 5.09907 ( 972) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 1.44926 ( 15) link_NAG-ASN : bond 0.00272 ( 10) link_NAG-ASN : angle 1.97241 ( 30) *********************** 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 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.339 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: A 1180 ASP cc_start: 0.7986 (m-30) cc_final: 0.7322 (t70) REVERT: A 2395 TYR cc_start: 0.7284 (t80) cc_final: 0.6861 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0871 time to fit residues: 16.7395 Evaluate side-chains 87 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 115 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS A1584 HIS ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN A2245 ASN A2455 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146641 restraints weight = 21595.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144292 restraints weight = 41685.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142238 restraints weight = 35158.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142051 restraints weight = 39356.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142033 restraints weight = 32129.550| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10662 Z= 0.138 Angle : 0.701 22.746 14536 Z= 0.355 Chirality : 0.044 0.251 1630 Planarity : 0.004 0.056 1894 Dihedral : 5.988 59.906 1742 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.23), residues: 1315 helix: 0.90 (0.42), residues: 159 sheet: -0.07 (0.30), residues: 308 loop : -0.91 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1392 TYR 0.023 0.001 TYR A1815 PHE 0.021 0.002 PHE A2428 TRP 0.016 0.001 TRP A2111 HIS 0.006 0.001 HIS A1791 Details of bonding type rmsd covalent geometry : bond 0.00312 (10611) covalent geometry : angle 0.63679 (14419) SS BOND : bond 0.01030 ( 36) SS BOND : angle 3.98160 ( 72) hydrogen bonds : bond 0.03949 ( 352) hydrogen bonds : angle 5.07786 ( 972) link_BETA1-4 : bond 0.00444 ( 5) link_BETA1-4 : angle 1.50816 ( 15) link_NAG-ASN : bond 0.00250 ( 10) link_NAG-ASN : angle 2.01429 ( 30) *********************** 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 130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.384 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: A 1180 ASP cc_start: 0.7966 (m-30) cc_final: 0.7292 (t70) REVERT: A 1307 THR cc_start: 0.8244 (m) cc_final: 0.7757 (p) REVERT: A 1811 MET cc_start: 0.7826 (mpp) cc_final: 0.7589 (mpp) REVERT: A 2395 TYR cc_start: 0.7194 (t80) cc_final: 0.6950 (t80) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.0851 time to fit residues: 16.3359 Evaluate side-chains 84 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1562 HIS ** A1705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1760 ASN A2245 ASN A2455 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147722 restraints weight = 21200.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147325 restraints weight = 37703.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146373 restraints weight = 30711.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145829 restraints weight = 29154.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145860 restraints weight = 25902.892| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.6240 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= 0.120 Angle : 0.670 19.554 14536 Z= 0.340 Chirality : 0.045 0.233 1630 Planarity : 0.004 0.050 1894 Dihedral : 5.954 59.258 1742 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.24), residues: 1315 helix: 0.92 (0.42), residues: 159 sheet: 0.13 (0.30), residues: 303 loop : -0.92 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1392 TYR 0.024 0.001 TYR A1815 PHE 0.017 0.001 PHE A2413 TRP 0.017 0.001 TRP A2111 HIS 0.007 0.001 HIS A1755 Details of bonding type rmsd covalent geometry : bond 0.00269 (10611) covalent geometry : angle 0.61916 (14419) SS BOND : bond 0.00649 ( 36) SS BOND : angle 3.43285 ( 72) hydrogen bonds : bond 0.03615 ( 352) hydrogen bonds : angle 5.06447 ( 972) link_BETA1-4 : bond 0.00475 ( 5) link_BETA1-4 : angle 1.39093 ( 15) link_NAG-ASN : bond 0.00267 ( 10) link_NAG-ASN : angle 1.93752 ( 30) ********************** 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 118 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.250 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: A 1180 ASP cc_start: 0.8007 (m-30) cc_final: 0.7311 (t70) REVERT: A 1307 THR cc_start: 0.8121 (m) cc_final: 0.7723 (p) REVERT: A 1381 LEU cc_start: 0.8759 (mm) cc_final: 0.8326 (mt) REVERT: A 1833 MET cc_start: -0.2720 (mmt) cc_final: -0.5803 (ppp) REVERT: A 2244 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7216 (tpp80) REVERT: A 2395 TYR cc_start: 0.7211 (t80) cc_final: 0.6754 (t80) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.0927 time to fit residues: 15.6242 Evaluate side-chains 90 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.7098 > 50: distance: 8 - 128: 27.622 distance: 11 - 125: 22.817 distance: 50 - 55: 27.382 distance: 55 - 56: 38.902 distance: 56 - 57: 17.905 distance: 57 - 58: 47.494 distance: 57 - 63: 11.582 distance: 59 - 60: 9.442 distance: 60 - 61: 10.679 distance: 60 - 62: 28.841 distance: 63 - 64: 40.072 distance: 63 - 69: 34.456 distance: 64 - 65: 33.323 distance: 64 - 67: 33.239 distance: 65 - 70: 35.319 distance: 67 - 68: 20.280 distance: 68 - 69: 27.639 distance: 70 - 71: 4.917 distance: 71 - 72: 62.355 distance: 71 - 74: 39.590 distance: 72 - 73: 41.570 distance: 72 - 76: 9.500 distance: 74 - 75: 11.797 distance: 76 - 77: 20.701 distance: 77 - 78: 42.278 distance: 77 - 80: 14.187 distance: 78 - 79: 46.037 distance: 78 - 82: 32.064 distance: 80 - 81: 20.507 distance: 82 - 83: 26.796 distance: 83 - 84: 18.809 distance: 83 - 86: 31.462 distance: 84 - 85: 29.597 distance: 84 - 90: 43.042 distance: 86 - 87: 30.245 distance: 87 - 88: 23.793 distance: 87 - 89: 37.503 distance: 90 - 91: 39.435 distance: 91 - 92: 39.212 distance: 91 - 94: 41.156 distance: 92 - 93: 10.970 distance: 92 - 99: 41.195 distance: 94 - 95: 11.529 distance: 95 - 96: 40.426 distance: 99 - 100: 48.399 distance: 100 - 101: 33.067 distance: 100 - 103: 34.592 distance: 101 - 102: 40.938 distance: 101 - 110: 23.152 distance: 103 - 104: 39.078 distance: 104 - 105: 30.030 distance: 105 - 106: 25.187 distance: 106 - 107: 25.635 distance: 107 - 108: 5.676 distance: 107 - 109: 32.427 distance: 110 - 111: 27.082 distance: 110 - 116: 31.246 distance: 111 - 112: 18.132 distance: 111 - 114: 22.939 distance: 112 - 113: 28.539 distance: 112 - 117: 40.694 distance: 114 - 115: 24.089 distance: 115 - 116: 46.845 distance: 117 - 118: 11.944 distance: 117 - 160: 31.363 distance: 118 - 119: 11.095 distance: 118 - 121: 16.073 distance: 119 - 120: 12.953 distance: 119 - 125: 35.273 distance: 120 - 157: 27.166 distance: 121 - 122: 13.048 distance: 121 - 123: 32.192 distance: 122 - 124: 36.140 distance: 125 - 126: 46.082 distance: 126 - 127: 29.553 distance: 127 - 133: 30.594 distance: 129 - 130: 39.468 distance: 130 - 132: 40.229