Starting phenix.real_space_refine on Tue Jul 7 04:38:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctn_45912/07_2026/9ctn_45912_trim.cif" } resolution = 3.11 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= 0.002 sd= 0.049 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 13791 2.51 5 N 3690 2.21 5 O 4093 1.98 5 H 21525 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43227 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21541 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1374, 21520 Classifications: {'peptide': 1374} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1310} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1374, 21520 Classifications: {'peptide': 1374} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1310} Chain breaks: 3 bond proxies already assigned to first conformer: 21726 Chain: "B" Number of atoms: 21542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1373, 21500 Classifications: {'peptide': 1373} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1309} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1373, 21500 Classifications: {'peptide': 1373} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1309} Chain breaks: 3 bond proxies already assigned to first conformer: 21684 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'6VG': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'6VG': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 13.74, per 1000 atoms: 0.32 Number of scatterers: 43227 At special positions: 0 Unit cell: (130.38, 113.42, 202.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 8 15.00 O 4093 8.00 N 3690 7.00 C 13791 6.00 H 21525 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 2.1 seconds 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 27 sheets defined 42.1% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.531A pdb=" N LEU A 900 " --> pdb=" O GLU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 929 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.553A pdb=" N LEU A 935 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1014 through 1024 removed outlier: 3.678A pdb=" N ARG A1024 " --> pdb=" O GLU A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.531A pdb=" N ASP A1058 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1089 removed outlier: 4.032A pdb=" N VAL A1088 " --> pdb=" O ASP A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1187 removed outlier: 3.609A pdb=" N LEU A1184 " --> pdb=" O MET A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1208 removed outlier: 3.742A pdb=" N ILE A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1203 " --> pdb=" O LYS A1199 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1231 Processing helix chain 'A' and resid 1241 through 1252 Processing helix chain 'A' and resid 1257 through 1267 removed outlier: 3.845A pdb=" N HIS A1267 " --> pdb=" O ARG A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1275 removed outlier: 3.869A pdb=" N LEU A1273 " --> pdb=" O VAL A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1282 removed outlier: 3.604A pdb=" N ALA A1281 " --> pdb=" O ILE A1278 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1282 " --> pdb=" O ILE A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1278 through 1282' Processing helix chain 'A' and resid 1284 through 1299 Processing helix chain 'A' and resid 1316 through 1324 Proline residue: A1322 - end of helix Processing helix chain 'A' and resid 1344 through 1348 removed outlier: 4.154A pdb=" N GLU A1348 " --> pdb=" O ASP A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.549A pdb=" N THR A1369 " --> pdb=" O ALA A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1384 Processing helix chain 'A' and resid 1386 through 1396 removed outlier: 3.688A pdb=" N LYS A1396 " --> pdb=" O THR A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1424 Processing helix chain 'A' and resid 1444 through 1455 Processing helix chain 'A' and resid 1496 through 1505 Processing helix chain 'A' and resid 1506 through 1510 removed outlier: 3.549A pdb=" N ASP A1509 " --> pdb=" O GLU A1506 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A1510 " --> pdb=" O LEU A1507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1506 through 1510' Processing helix chain 'A' and resid 1526 through 1539 removed outlier: 3.761A pdb=" N ARG A1532 " --> pdb=" O LEU A1528 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A1536 " --> pdb=" O ARG A1532 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1564 through 1574 removed outlier: 4.014A pdb=" N LYS A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1594 through 1600 removed outlier: 3.609A pdb=" N GLN A1599 " --> pdb=" O ALA A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1630 Processing helix chain 'A' and resid 1636 through 1641 Processing helix chain 'A' and resid 1657 through 1665 removed outlier: 3.551A pdb=" N ILE A1661 " --> pdb=" O ASN A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1673 Processing helix chain 'A' and resid 1674 through 1678 Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.505A pdb=" N ALA A1731 " --> pdb=" O LEU A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1745 removed outlier: 4.311A pdb=" N ALA A1736 " --> pdb=" O THR A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1763 through 1776 Processing helix chain 'A' and resid 1786 through 1797 Processing helix chain 'A' and resid 1801 through 1803 No H-bonds generated for 'chain 'A' and resid 1801 through 1803' Processing helix chain 'A' and resid 1812 through 1821 removed outlier: 3.965A pdb=" N TYR A1816 " --> pdb=" O SER A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1844 Processing helix chain 'A' and resid 1860 through 1868 Processing helix chain 'A' and resid 1876 through 1885 Processing helix chain 'A' and resid 1886 through 1902 removed outlier: 3.753A pdb=" N LEU A1892 " --> pdb=" O GLU A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1916 No H-bonds generated for 'chain 'A' and resid 1914 through 1916' Processing helix chain 'A' and resid 1917 through 1928 Processing helix chain 'A' and resid 1976 through 1989 removed outlier: 3.762A pdb=" N GLU A1980 " --> pdb=" O GLY A1976 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A1984 " --> pdb=" O GLU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2017 Processing helix chain 'A' and resid 2029 through 2042 Processing helix chain 'A' and resid 2060 through 2064 removed outlier: 3.539A pdb=" N MET A2064 " --> pdb=" O PHE A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2070 Processing helix chain 'A' and resid 2077 through 2089 Processing helix chain 'A' and resid 2091 through 2096 Processing helix chain 'A' and resid 2106 through 2108 No H-bonds generated for 'chain 'A' and resid 2106 through 2108' Processing helix chain 'A' and resid 2114 through 2134 removed outlier: 3.820A pdb=" N GLU A2129 " --> pdb=" O GLU A2125 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A2131 " --> pdb=" O ILE A2127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A2132 " --> pdb=" O CYS A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2170 through 2183 removed outlier: 3.734A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A2180 " --> pdb=" O SER A2176 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A2183 " --> pdb=" O ASP A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2220 removed outlier: 3.551A pdb=" N LEU A2213 " --> pdb=" O VAL A2209 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2238 Processing helix chain 'A' and resid 2242 through 2254 removed outlier: 3.698A pdb=" N GLU A2252 " --> pdb=" O LYS A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2266 removed outlier: 3.896A pdb=" N GLN A2265 " --> pdb=" O THR A2261 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A2266 " --> pdb=" O LYS A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2278 removed outlier: 3.709A pdb=" N LYS A2277 " --> pdb=" O ARG A2273 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A2278 " --> pdb=" O SER A2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 removed outlier: 3.677A pdb=" N LEU B 900 " --> pdb=" O GLU B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 928 removed outlier: 3.562A pdb=" N ALA B 925 " --> pdb=" O TRP B 921 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 935 removed outlier: 3.729A pdb=" N LEU B 935 " --> pdb=" O PHE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 998 removed outlier: 4.355A pdb=" N HIS B 996 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1014 through 1024 removed outlier: 3.508A pdb=" N PHE B1021 " --> pdb=" O ILE B1017 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B1024 " --> pdb=" O GLU B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1067 removed outlier: 4.001A pdb=" N MET B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR B1064 " --> pdb=" O VAL B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1187 Processing helix chain 'B' and resid 1194 through 1208 Processing helix chain 'B' and resid 1218 through 1231 Processing helix chain 'B' and resid 1240 through 1249 removed outlier: 3.924A pdb=" N GLU B1244 " --> pdb=" O HIS B1240 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1269 removed outlier: 3.519A pdb=" N MET B1264 " --> pdb=" O ASP B1260 " (cutoff:3.500A) Processing helix chain 'B' and resid 1269 through 1275 removed outlier: 4.270A pdb=" N LEU B1273 " --> pdb=" O VAL B1269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP B1274 " --> pdb=" O ARG B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1299 removed outlier: 3.602A pdb=" N ASN B1298 " --> pdb=" O THR B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1324 Proline residue: B1322 - end of helix Processing helix chain 'B' and resid 1325 through 1328 Processing helix chain 'B' and resid 1343 through 1347 Processing helix chain 'B' and resid 1365 through 1369 Processing helix chain 'B' and resid 1386 through 1397 removed outlier: 3.734A pdb=" N THR B1392 " --> pdb=" O ASP B1388 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B1396 " --> pdb=" O THR B1392 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B1397 " --> pdb=" O GLU B1393 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1420 Processing helix chain 'B' and resid 1444 through 1455 removed outlier: 3.638A pdb=" N ALA B1450 " --> pdb=" O ALA B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1506 Processing helix chain 'B' and resid 1507 through 1510 Processing helix chain 'B' and resid 1526 through 1539 removed outlier: 3.560A pdb=" N ARG B1532 " --> pdb=" O LEU B1528 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B1536 " --> pdb=" O ARG B1532 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B1537 " --> pdb=" O SER B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1564 through 1574 removed outlier: 3.631A pdb=" N LYS B1568 " --> pdb=" O SER B1564 " (cutoff:3.500A) Processing helix chain 'B' and resid 1596 through 1600 Processing helix chain 'B' and resid 1626 through 1630 Processing helix chain 'B' and resid 1636 through 1641 removed outlier: 3.841A pdb=" N LYS B1639 " --> pdb=" O LEU B1636 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1665 removed outlier: 3.564A pdb=" N ILE B1661 " --> pdb=" O ASN B1657 " (cutoff:3.500A) Processing helix chain 'B' and resid 1674 through 1678 removed outlier: 3.585A pdb=" N PHE B1678 " --> pdb=" O GLU B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1731 Processing helix chain 'B' and resid 1733 through 1745 Processing helix chain 'B' and resid 1763 through 1776 Processing helix chain 'B' and resid 1786 through 1797 removed outlier: 3.557A pdb=" N THR B1790 " --> pdb=" O ASN B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1801 through 1803 No H-bonds generated for 'chain 'B' and resid 1801 through 1803' Processing helix chain 'B' and resid 1812 through 1821 removed outlier: 3.564A pdb=" N TYR B1816 " --> pdb=" O SER B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1844 removed outlier: 3.590A pdb=" N LYS B1839 " --> pdb=" O GLY B1835 " (cutoff:3.500A) Processing helix chain 'B' and resid 1859 through 1868 Processing helix chain 'B' and resid 1876 through 1885 removed outlier: 3.522A pdb=" N SER B1884 " --> pdb=" O ALA B1880 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1902 removed outlier: 3.766A pdb=" N LEU B1892 " --> pdb=" O GLU B1888 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1928 Processing helix chain 'B' and resid 1975 through 1989 removed outlier: 3.563A pdb=" N GLU B1980 " --> pdb=" O GLY B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 2003 through 2017 Processing helix chain 'B' and resid 2029 through 2044 Processing helix chain 'B' and resid 2060 through 2064 Processing helix chain 'B' and resid 2065 through 2070 Processing helix chain 'B' and resid 2072 through 2077 removed outlier: 3.567A pdb=" N LYS B2076 " --> pdb=" O PRO B2072 " (cutoff:3.500A) Processing helix chain 'B' and resid 2079 through 2087 Processing helix chain 'B' and resid 2091 through 2096 Processing helix chain 'B' and resid 2105 through 2110 Processing helix chain 'B' and resid 2114 through 2134 Processing helix chain 'B' and resid 2170 through 2183 removed outlier: 3.679A pdb=" N PHE B2180 " --> pdb=" O SER B2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 2207 through 2220 removed outlier: 4.569A pdb=" N LEU B2213 " --> pdb=" O VAL B2209 " (cutoff:3.500A) Processing helix chain 'B' and resid 2224 through 2228 Processing helix chain 'B' and resid 2233 through 2238 Processing helix chain 'B' and resid 2242 through 2255 Processing helix chain 'B' and resid 2260 through 2265 removed outlier: 3.603A pdb=" N GLN B2265 " --> pdb=" O THR B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2278 removed outlier: 3.810A pdb=" N VAL B2276 " --> pdb=" O LEU B2272 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B2277 " --> pdb=" O ARG B2273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 887 through 891 Processing sheet with id=AA2, first strand: chain 'A' and resid 903 through 905 Processing sheet with id=AA3, first strand: chain 'A' and resid 961 through 962 removed outlier: 6.594A pdb=" N PHE A 969 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 980 " --> pdb=" O PHE A 969 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 971 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER A 980 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 942 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 936 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN A 938 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A1083 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 940 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A1081 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A1073 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS A1125 " --> pdb=" O THR A1077 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A1079 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER A1123 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A1081 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A1121 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR A1083 " --> pdb=" O VAL A1119 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A1119 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A1105 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1011 through 1013 Processing sheet with id=AA5, first strand: chain 'A' and resid 1048 through 1049 removed outlier: 3.925A pdb=" N GLN A1101 " --> pdb=" O TRP A1049 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1485 through 1488 removed outlier: 6.427A pdb=" N ILE A1485 " --> pdb=" O TRP A1517 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A1519 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A1487 " --> pdb=" O VAL A1519 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A1516 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A1546 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A1518 " --> pdb=" O ILE A1546 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A1548 " --> pdb=" O LEU A1518 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A1520 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN A1578 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS A1545 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE A1580 " --> pdb=" O CYS A1545 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN A1547 " --> pdb=" O PHE A1580 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TYR A1577 " --> pdb=" O TYR A1588 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A1588 " --> pdb=" O TYR A1577 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A1140 " --> pdb=" O ILE A1593 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A1143 " --> pdb=" O VAL A2188 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL A2188 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A2140 " --> pdb=" O THR A2189 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER A2191 " --> pdb=" O THR A2140 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN A2142 " --> pdb=" O SER A2191 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL A2193 " --> pdb=" O GLN A2142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1485 through 1488 removed outlier: 6.427A pdb=" N ILE A1485 " --> pdb=" O TRP A1517 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A1519 " --> pdb=" O ILE A1485 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A1487 " --> pdb=" O VAL A1519 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU A1516 " --> pdb=" O ARG A1544 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A1546 " --> pdb=" O LEU A1516 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A1518 " --> pdb=" O ILE A1546 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A1548 " --> pdb=" O LEU A1518 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A1520 " --> pdb=" O ILE A1548 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ASN A1578 " --> pdb=" O LEU A1543 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS A1545 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE A1580 " --> pdb=" O CYS A1545 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN A1547 " --> pdb=" O PHE A1580 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TYR A1577 " --> pdb=" O TYR A1588 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A1588 " --> pdb=" O TYR A1577 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A1140 " --> pdb=" O ILE A1593 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A1143 " --> pdb=" O VAL A2188 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL A2188 " --> pdb=" O PHE A1143 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A2193 " --> pdb=" O TYR A2167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1351 through 1355 removed outlier: 3.744A pdb=" N ASP A1339 " --> pdb=" O MET A1354 " (cutoff:3.500A) removed outlier: 11.456A pdb=" N VAL A1303 " --> pdb=" O CYS A1372 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A1374 " --> pdb=" O VAL A1303 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A1305 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A1376 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A1307 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP A1373 " --> pdb=" O PHE A1403 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU A1405 " --> pdb=" O ASP A1373 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A1375 " --> pdb=" O LEU A1405 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A1407 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A1469 " --> pdb=" O PRO A1464 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET A1471 " --> pdb=" O HIS A1462 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS A1462 " --> pdb=" O MET A1471 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A1473 " --> pdb=" O ILE A1460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1602 through 1604 Processing sheet with id=AB1, first strand: chain 'A' and resid 1607 through 1611 Processing sheet with id=AB2, first strand: chain 'A' and resid 1710 through 1714 removed outlier: 6.706A pdb=" N SER A1689 " --> pdb=" O TYR A1652 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA A1654 " --> pdb=" O GLU A1687 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLU A1687 " --> pdb=" O ALA A1654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1710 through 1714 removed outlier: 4.329A pdb=" N ILE A1934 " --> pdb=" O LEU A1656 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A1913 " --> pdb=" O LYS A1937 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1805 through 1807 removed outlier: 7.812A pdb=" N CYS A1806 " --> pdb=" O ILE A1780 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A1782 " --> pdb=" O CYS A1806 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A1755 " --> pdb=" O VAL A1826 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP A1827 " --> pdb=" O LYS A1848 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2019 through 2024 removed outlier: 6.759A pdb=" N LEU A1993 " --> pdb=" O GLU A2021 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A2023 " --> pdb=" O LEU A1993 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A1995 " --> pdb=" O LEU A2023 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A1967 " --> pdb=" O VAL A2046 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A2048 " --> pdb=" O SER A1967 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL A2100 " --> pdb=" O GLY A2047 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A2049 " --> pdb=" O VAL A2100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 885 through 891 removed outlier: 3.587A pdb=" N THR B 956 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 982 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASN B 941 " --> pdb=" O VAL B 982 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B1080 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 943 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B1078 " --> pdb=" O GLN B 943 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP B1044 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA B1038 " --> pdb=" O ASP B1044 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B1046 " --> pdb=" O GLN B1036 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 885 through 891 removed outlier: 3.587A pdb=" N THR B 956 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 982 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASN B 941 " --> pdb=" O VAL B 982 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU B1080 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN B 943 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B1078 " --> pdb=" O GLN B 943 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN B1073 " --> pdb=" O ALA B1129 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS B1125 " --> pdb=" O THR B1077 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 908 through 909 removed outlier: 3.541A pdb=" N ARG B 908 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1485 through 1488 removed outlier: 6.354A pdb=" N ILE B1485 " --> pdb=" O TRP B1517 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B1519 " --> pdb=" O ILE B1485 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B1487 " --> pdb=" O VAL B1519 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B1516 " --> pdb=" O ARG B1544 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B1546 " --> pdb=" O LEU B1516 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1518 " --> pdb=" O ILE B1546 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE B1548 " --> pdb=" O LEU B1518 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B1520 " --> pdb=" O ILE B1548 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASN B1578 " --> pdb=" O LEU B1543 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B1545 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE B1580 " --> pdb=" O CYS B1545 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLN B1547 " --> pdb=" O PHE B1580 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N TYR B1577 " --> pdb=" O TYR B1588 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B1588 " --> pdb=" O TYR B1577 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B2188 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B2140 " --> pdb=" O THR B2189 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER B2191 " --> pdb=" O THR B2140 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN B2142 " --> pdb=" O SER B2191 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL B2193 " --> pdb=" O GLN B2142 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP B2143 " --> pdb=" O SER B2103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1485 through 1488 removed outlier: 6.354A pdb=" N ILE B1485 " --> pdb=" O TRP B1517 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B1519 " --> pdb=" O ILE B1485 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B1487 " --> pdb=" O VAL B1519 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B1516 " --> pdb=" O ARG B1544 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B1546 " --> pdb=" O LEU B1516 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1518 " --> pdb=" O ILE B1546 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE B1548 " --> pdb=" O LEU B1518 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B1520 " --> pdb=" O ILE B1548 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASN B1578 " --> pdb=" O LEU B1543 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B1545 " --> pdb=" O ASN B1578 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE B1580 " --> pdb=" O CYS B1545 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLN B1547 " --> pdb=" O PHE B1580 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N TYR B1577 " --> pdb=" O TYR B1588 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B1588 " --> pdb=" O TYR B1577 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B2188 " --> pdb=" O PHE B1143 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B2193 " --> pdb=" O TYR B2167 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1332 through 1334 removed outlier: 3.535A pdb=" N ASP B1339 " --> pdb=" O MET B1354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1332 through 1334 removed outlier: 11.581A pdb=" N VAL B1303 " --> pdb=" O CYS B1372 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU B1374 " --> pdb=" O VAL B1303 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU B1305 " --> pdb=" O LEU B1374 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL B1376 " --> pdb=" O GLU B1305 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B1307 " --> pdb=" O VAL B1376 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS B1378 " --> pdb=" O LEU B1307 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B1309 " --> pdb=" O LYS B1378 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B1373 " --> pdb=" O PHE B1403 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU B1405 " --> pdb=" O ASP B1373 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B1375 " --> pdb=" O LEU B1405 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU B1407 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B1377 " --> pdb=" O LEU B1407 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASN B1409 " --> pdb=" O LEU B1377 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG B1475 " --> pdb=" O GLN B1459 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLN B1459 " --> pdb=" O ARG B1475 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1602 through 1604 Processing sheet with id=AC5, first strand: chain 'B' and resid 1607 through 1611 Processing sheet with id=AC6, first strand: chain 'B' and resid 1711 through 1714 removed outlier: 6.803A pdb=" N SER B1689 " --> pdb=" O TYR B1652 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA B1654 " --> pdb=" O GLU B1687 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU B1687 " --> pdb=" O ALA B1654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1711 through 1714 removed outlier: 4.498A pdb=" N ILE B1934 " --> pdb=" O LEU B1656 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA B1911 " --> pdb=" O VAL B1935 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS B1937 " --> pdb=" O ALA B1911 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B1913 " --> pdb=" O LYS B1937 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1805 through 1807 removed outlier: 7.811A pdb=" N CYS B1806 " --> pdb=" O ILE B1780 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B1782 " --> pdb=" O CYS B1806 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B1755 " --> pdb=" O VAL B1826 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP B1827 " --> pdb=" O LYS B1848 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 2019 through 2024 removed outlier: 6.965A pdb=" N SER B1967 " --> pdb=" O GLY B2048 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N PHE B2050 " --> pdb=" O SER B1967 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B1969 " --> pdb=" O PHE B2050 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY B2047 " --> pdb=" O HIS B2098 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL B2100 " --> pdb=" O GLY B2047 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B2049 " --> pdb=" O VAL B2100 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2540 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: 12.88 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21489 1.03 - 1.23: 343 1.23 - 1.43: 8856 1.43 - 1.63: 12792 1.63 - 1.82: 212 Bond restraints: 43692 Sorted by residual: bond pdb=" O26 6VG A2302 " pdb=" P24 6VG A2302 " ideal model delta sigma weight residual 1.655 1.504 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" O26 6VG B2302 " pdb=" P24 6VG B2302 " ideal model delta sigma weight residual 1.655 1.504 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O27 6VG A2302 " pdb=" P24 6VG A2302 " ideal model delta sigma weight residual 1.726 1.605 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" O27 6VG B2302 " pdb=" P24 6VG B2302 " ideal model delta sigma weight residual 1.726 1.605 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C1 6VG A2302 " pdb=" S1 6VG A2302 " ideal model delta sigma weight residual 1.781 1.706 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 43687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 79000 3.63 - 7.26: 60 7.26 - 10.90: 2 10.90 - 14.53: 5 14.53 - 18.16: 3 Bond angle restraints: 79070 Sorted by residual: angle pdb=" O23 6VG B2302 " pdb=" P24 6VG B2302 " pdb=" O26 6VG B2302 " ideal model delta sigma weight residual 102.01 120.17 -18.16 3.00e+00 1.11e-01 3.66e+01 angle pdb=" O23 6VG A2302 " pdb=" P24 6VG A2302 " pdb=" O26 6VG A2302 " ideal model delta sigma weight residual 102.01 120.17 -18.16 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C2 6VG A2302 " pdb=" C1 6VG A2302 " pdb=" S1 6VG A2302 " ideal model delta sigma weight residual 113.34 131.23 -17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O1 6VG A2302 " pdb=" C1 6VG A2302 " pdb=" S1 6VG A2302 " ideal model delta sigma weight residual 123.13 108.90 14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" O1 6VG B2302 " pdb=" C1 6VG B2302 " pdb=" S1 6VG B2302 " ideal model delta sigma weight residual 123.13 109.43 13.70 3.00e+00 1.11e-01 2.08e+01 ... (remaining 79065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 19731 35.61 - 71.21: 730 71.21 - 106.82: 20 106.82 - 142.43: 4 142.43 - 178.03: 6 Dihedral angle restraints: 20491 sinusoidal: 11208 harmonic: 9283 Sorted by residual: dihedral pdb=" C39 6VG B2302 " pdb=" C42 6VG B2302 " pdb=" N41 6VG B2302 " pdb=" C43 6VG B2302 " ideal model delta sinusoidal sigma weight residual 84.69 -97.28 -178.03 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C37 6VG B2302 " pdb=" C38 6VG B2302 " pdb=" C39 6VG B2302 " pdb=" N41 6VG B2302 " ideal model delta sinusoidal sigma weight residual 122.91 -73.65 -163.44 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C37 6VG B2302 " pdb=" C38 6VG B2302 " pdb=" C39 6VG B2302 " pdb=" O40 6VG B2302 " ideal model delta sinusoidal sigma weight residual -56.39 106.04 -162.43 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 20488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2006 0.028 - 0.057: 929 0.057 - 0.085: 216 0.085 - 0.114: 151 0.114 - 0.142: 45 Chirality restraints: 3347 Sorted by residual: chirality pdb=" CA VAL B2055 " pdb=" N VAL B2055 " pdb=" C VAL B2055 " pdb=" CB VAL B2055 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA PRO B1734 " pdb=" N PRO B1734 " pdb=" C PRO B1734 " pdb=" CB PRO B1734 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA VAL A2239 " pdb=" N VAL A2239 " pdb=" C VAL A2239 " pdb=" CB VAL A2239 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 3344 not shown) Planarity restraints: 6477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 6VG B2302 " -0.161 2.00e-02 2.50e+03 9.30e-02 8.66e+01 pdb=" C2 6VG B2302 " 0.055 2.00e-02 2.50e+03 pdb=" O1 6VG B2302 " 0.061 2.00e-02 2.50e+03 pdb=" S1 6VG B2302 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 6VG A2302 " -0.065 2.00e-02 2.50e+03 7.22e-02 6.52e+01 pdb=" C34 6VG A2302 " 0.020 2.00e-02 2.50e+03 pdb=" C37 6VG A2302 " -0.088 2.00e-02 2.50e+03 pdb=" N36 6VG A2302 " 0.115 2.00e-02 2.50e+03 pdb=" O35 6VG A2302 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 6VG B2302 " 0.058 2.00e-02 2.50e+03 6.27e-02 4.92e+01 pdb=" C39 6VG B2302 " -0.023 2.00e-02 2.50e+03 pdb=" C42 6VG B2302 " 0.077 2.00e-02 2.50e+03 pdb=" N41 6VG B2302 " -0.099 2.00e-02 2.50e+03 pdb=" O40 6VG B2302 " -0.013 2.00e-02 2.50e+03 ... (remaining 6474 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 804 2.09 - 2.71: 72766 2.71 - 3.34: 125285 3.34 - 3.97: 162986 3.97 - 4.60: 257939 Nonbonded interactions: 619780 Sorted by model distance: nonbonded pdb=" OE1 GLU B1888 " pdb=" H GLU B1888 " model vdw 1.457 2.450 nonbonded pdb=" OE1 GLU B1196 " pdb=" H GLU B1196 " model vdw 1.596 2.450 nonbonded pdb=" O ASP A1373 " pdb=" H PHE A1403 " model vdw 1.603 2.450 nonbonded pdb=" O ARG B1803 " pdb=" HH TYR B1816 " model vdw 1.606 2.450 nonbonded pdb=" OE2 GLU A1980 " pdb=" HH TYR A2005 " model vdw 1.615 2.450 ... (remaining 619775 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 'A' and (resid 883 through 1597 or resid 1599 through 1817 or resid 1819 \ through 2153 or resid 2161 through 2240 or (resid 2241 and (name N or name CA or \ name C or name O or name CB or name OG or name H or name HB2 or name HB3)) or r \ esid 2242 through 2302)) selection = (chain 'B' and (resid 883 through 1597 or resid 1599 through 1817 or resid 1819 \ through 2302)) } 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=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.340 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 50.850 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.004 0.151 22169 Z= 0.175 Angle : 0.634 18.159 30026 Z= 0.328 Chirality : 0.039 0.142 3347 Planarity : 0.005 0.093 3861 Dihedral : 18.058 178.033 8220 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 0.85 % Allowed : 25.87 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -1.22 (0.16), residues: 2734 helix: -0.18 (0.17), residues: 933 sheet: -1.26 (0.23), residues: 484 loop : -0.99 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1929 TYR 0.018 0.001 TYR A1018 PHE 0.016 0.001 PHE A1218 TRP 0.015 0.001 TRP B1379 HIS 0.004 0.001 HIS A1511 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (22167) covalent geometry : angle 0.63359 / 0.33 (30026) hydrogen bonds : bond 0.24466 / 15.92 ( 865) hydrogen bonds : angle 8.58893 / 6.00 ( 2540) Misc. bond : bond 0.04752 / 2.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1262 LEU cc_start: 0.8770 (tp) cc_final: 0.8375 (tp) REVERT: A 1304 MET cc_start: 0.8028 (ttt) cc_final: 0.7813 (ttt) REVERT: A 1329 SER cc_start: 0.8968 (m) cc_final: 0.8695 (p) REVERT: A 1354 MET cc_start: 0.7112 (mtp) cc_final: 0.6885 (mtp) REVERT: A 1383 MET cc_start: 0.8174 (mtp) cc_final: 0.7901 (mtp) REVERT: A 1439 MET cc_start: 0.9263 (mpt) cc_final: 0.8720 (mpt) REVERT: A 1556 ASN cc_start: 0.8625 (t0) cc_final: 0.8393 (t0) REVERT: A 1827 ASP cc_start: 0.8145 (m-30) cc_final: 0.7725 (m-30) REVERT: A 1943 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7796 (mtm110) REVERT: A 2214 ARG cc_start: 0.7547 (ttm110) cc_final: 0.6913 (ttp-110) REVERT: B 989 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7544 (ttp80) REVERT: B 1068 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8290 (mmtp) REVERT: B 1302 GLN cc_start: 0.7993 (tp40) cc_final: 0.7652 (tp40) REVERT: B 1340 GLN cc_start: 0.7707 (mm110) cc_final: 0.7437 (mm110) REVERT: B 1471 MET cc_start: 0.8485 (ttp) cc_final: 0.8283 (ttm) REVERT: B 1569 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7387 (mp0) REVERT: B 1675 GLU cc_start: 0.8459 (pt0) cc_final: 0.8156 (tt0) REVERT: B 1868 THR cc_start: 0.8757 (m) cc_final: 0.8377 (p) REVERT: B 1906 LYS cc_start: 0.8460 (mtmp) cc_final: 0.8013 (mttp) REVERT: B 1930 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: B 2043 MET cc_start: 0.8650 (mtt) cc_final: 0.8445 (mtt) REVERT: B 2101 MET cc_start: 0.9116 (mmt) cc_final: 0.8770 (mmt) REVERT: B 2181 MET cc_start: 0.8203 (mtt) cc_final: 0.7703 (mtt) REVERT: B 2243 MET cc_start: 0.7541 (ttp) cc_final: 0.7212 (ttm) outliers start: 20 outliers final: 13 residues processed: 294 average time/residue: 0.4117 time to fit residues: 183.7109 Evaluate side-chains 249 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2075 SER Chi-restraints excluded: chain A residue 2237 MET Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1531 LEU Chi-restraints excluded: chain B residue 1930 GLU Chi-restraints excluded: chain B residue 1961 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1240 HIS A1511 HIS B1267 HIS ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2039 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.082093 restraints weight = 112475.841| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.15 r_work: 0.2809 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22169 Z= 0.199 Angle : 0.605 6.381 30026 Z= 0.317 Chirality : 0.042 0.155 3347 Planarity : 0.005 0.052 3861 Dihedral : 9.890 161.551 3038 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 1.71 % Allowed : 23.57 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -1.04 (0.16), residues: 2734 helix: 0.07 (0.16), residues: 996 sheet: -1.27 (0.23), residues: 490 loop : -0.96 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1261 TYR 0.023 0.001 TYR A1018 PHE 0.018 0.001 PHE A1567 TRP 0.015 0.001 TRP B1259 HIS 0.005 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (22167) covalent geometry : angle 0.60516 / 0.32 (30026) hydrogen bonds : bond 0.06351 / 4.25 ( 865) hydrogen bonds : angle 5.84608 / 4.12 ( 2540) Misc. bond : bond 0.00418 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8572 (t0) cc_final: 0.8112 (p0) REVERT: A 1293 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 1304 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8144 (ttt) REVERT: A 1439 MET cc_start: 0.9372 (mpt) cc_final: 0.8764 (mpt) REVERT: A 1556 ASN cc_start: 0.8443 (t0) cc_final: 0.8183 (t0) REVERT: A 1751 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: A 1827 ASP cc_start: 0.8453 (m-30) cc_final: 0.8208 (m-30) REVERT: A 1943 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7828 (mtm110) REVERT: B 987 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 989 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.8018 (ttp80) REVERT: B 1068 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8477 (mmtp) REVERT: B 1302 GLN cc_start: 0.8373 (tp40) cc_final: 0.8100 (tp40) REVERT: B 1340 GLN cc_start: 0.7881 (mm110) cc_final: 0.7679 (mm110) REVERT: B 1343 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7166 (m) REVERT: B 1675 GLU cc_start: 0.8639 (pt0) cc_final: 0.8252 (tt0) REVERT: B 1906 LYS cc_start: 0.8823 (mtmp) cc_final: 0.8524 (mttp) REVERT: B 2101 MET cc_start: 0.9175 (mmt) cc_final: 0.8972 (mmt) outliers start: 40 outliers final: 24 residues processed: 284 average time/residue: 0.3991 time to fit residues: 172.1505 Evaluate side-chains 268 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1183 TRP Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1308 GLU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1668 ILE Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1751 GLN Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1511 HIS Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 2095 THR Chi-restraints excluded: chain B residue 2251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 215 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1267 HIS ** B1462 HIS ** 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 = 0.3387 r_free = 0.3387 target = 0.115171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.082185 restraints weight = 107115.134| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.16 r_work: 0.2813 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22169 Z= 0.167 Angle : 0.565 7.219 30026 Z= 0.292 Chirality : 0.041 0.143 3347 Planarity : 0.005 0.065 3861 Dihedral : 9.286 162.509 3024 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 1.96 % Allowed : 22.34 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.86 (0.16), residues: 2734 helix: 0.39 (0.16), residues: 982 sheet: -1.28 (0.23), residues: 484 loop : -0.95 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1951 TYR 0.024 0.001 TYR A1018 PHE 0.018 0.001 PHE A1567 TRP 0.013 0.001 TRP A1889 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (22167) covalent geometry : angle 0.56487 / 0.29 (30026) hydrogen bonds : bond 0.04646 / 3.14 ( 865) hydrogen bonds : angle 5.13010 / 3.61 ( 2540) Misc. bond : bond 0.00054 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8636 (t0) cc_final: 0.8035 (p0) REVERT: A 1293 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 1439 MET cc_start: 0.9343 (mpt) cc_final: 0.8724 (mpt) REVERT: A 1556 ASN cc_start: 0.8382 (t0) cc_final: 0.8034 (t0) REVERT: A 1827 ASP cc_start: 0.8652 (m-30) cc_final: 0.8400 (m-30) REVERT: A 1943 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7861 (mtm110) REVERT: A 2211 GLN cc_start: 0.7939 (tp40) cc_final: 0.7731 (tp40) REVERT: A 2214 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7165 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 987 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: B 989 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.8054 (ttp80) REVERT: B 1068 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8350 (mmtp) REVERT: B 1207 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8366 (ttpp) REVERT: B 1302 GLN cc_start: 0.8587 (tp40) cc_final: 0.8306 (tp40) REVERT: B 1304 MET cc_start: 0.8249 (ttt) cc_final: 0.7438 (ttt) REVERT: B 1326 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8241 (mt-10) REVERT: B 1340 GLN cc_start: 0.8091 (mm110) cc_final: 0.7888 (mm110) REVERT: B 1343 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7099 (m) REVERT: B 1675 GLU cc_start: 0.8585 (pt0) cc_final: 0.8212 (tt0) REVERT: B 1906 LYS cc_start: 0.8871 (mtmp) cc_final: 0.8538 (mttp) REVERT: B 1995 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8582 (mt) REVERT: B 2101 MET cc_start: 0.9167 (mmt) cc_final: 0.8912 (mmt) outliers start: 46 outliers final: 28 residues processed: 291 average time/residue: 0.4044 time to fit residues: 178.7986 Evaluate side-chains 275 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1183 TRP Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1668 ILE Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 2009 LYS Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2213 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1511 HIS Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2015 GLN Chi-restraints excluded: chain B residue 2070 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 203 optimal weight: 0.0060 chunk 213 optimal weight: 2.9990 chunk 158 optimal weight: 0.0010 chunk 173 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.0020 chunk 200 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1073 GLN ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.081979 restraints weight = 115541.689| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.24 r_work: 0.2800 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22169 Z= 0.135 Angle : 0.536 8.859 30026 Z= 0.274 Chirality : 0.040 0.139 3347 Planarity : 0.004 0.061 3861 Dihedral : 8.797 167.424 3024 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.58 % Allowed : 22.72 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.69 (0.16), residues: 2734 helix: 0.60 (0.17), residues: 979 sheet: -1.32 (0.23), residues: 482 loop : -0.85 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1818 TYR 0.025 0.001 TYR A1018 PHE 0.018 0.001 PHE B1243 TRP 0.013 0.001 TRP A1889 HIS 0.004 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22167) covalent geometry : angle 0.53574 / 0.27 (30026) hydrogen bonds : bond 0.03980 / 2.71 ( 865) hydrogen bonds : angle 4.86724 / 3.43 ( 2540) Misc. bond : bond 0.00036 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8640 (t0) cc_final: 0.8031 (p0) REVERT: A 1178 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7015 (mm-40) REVERT: A 1252 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 1258 TYR cc_start: 0.7939 (t80) cc_final: 0.7625 (t80) REVERT: A 1293 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 1313 ARG cc_start: 0.8524 (mmt180) cc_final: 0.8271 (mmt90) REVERT: A 1510 SER cc_start: 0.8982 (t) cc_final: 0.8527 (p) REVERT: A 1556 ASN cc_start: 0.8372 (t0) cc_final: 0.8045 (t0) REVERT: A 1827 ASP cc_start: 0.8688 (m-30) cc_final: 0.8443 (m-30) REVERT: A 1943 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7863 (mtm110) REVERT: A 2211 GLN cc_start: 0.8097 (tp40) cc_final: 0.7810 (tp40) REVERT: A 2214 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8155 (tt) REVERT: B 987 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: B 989 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8099 (ttp80) REVERT: B 1068 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8333 (mmtp) REVERT: B 1207 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8398 (ttpp) REVERT: B 1302 GLN cc_start: 0.8632 (tp40) cc_final: 0.8106 (tp40) REVERT: B 1304 MET cc_start: 0.8310 (ttt) cc_final: 0.7522 (ttt) REVERT: B 1326 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8290 (mt-10) REVERT: B 1343 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.7079 (m) REVERT: B 1511 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7792 (t-170) REVERT: B 1675 GLU cc_start: 0.8520 (pt0) cc_final: 0.8063 (tt0) REVERT: B 1906 LYS cc_start: 0.8879 (mtmp) cc_final: 0.8541 (mttp) REVERT: B 2101 MET cc_start: 0.9175 (mmt) cc_final: 0.8959 (mmt) outliers start: 37 outliers final: 25 residues processed: 275 average time/residue: 0.4065 time to fit residues: 168.1536 Evaluate side-chains 270 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1578 ASN Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1511 HIS Chi-restraints excluded: chain B residue 1531 LEU Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 249 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 970 GLN ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.082656 restraints weight = 110183.196| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.19 r_work: 0.2822 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22169 Z= 0.114 Angle : 0.515 6.689 30026 Z= 0.263 Chirality : 0.040 0.137 3347 Planarity : 0.004 0.048 3861 Dihedral : 8.507 175.142 3024 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 1.96 % Allowed : 21.91 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.53 (0.16), residues: 2734 helix: 0.78 (0.17), residues: 979 sheet: -1.31 (0.23), residues: 474 loop : -0.77 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1818 TYR 0.023 0.001 TYR A1018 PHE 0.018 0.001 PHE A1243 TRP 0.013 0.001 TRP A1889 HIS 0.003 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (22167) covalent geometry : angle 0.51532 / 0.26 (30026) hydrogen bonds : bond 0.03682 / 2.51 ( 865) hydrogen bonds : angle 4.70098 / 3.31 ( 2540) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8638 (t0) cc_final: 0.8021 (p0) REVERT: A 1178 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6995 (mm-40) REVERT: A 1252 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 1258 TYR cc_start: 0.7958 (t80) cc_final: 0.7660 (t80) REVERT: A 1262 LEU cc_start: 0.8623 (mt) cc_final: 0.8190 (mp) REVERT: A 1293 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 1313 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8230 (mmt90) REVERT: A 1510 SER cc_start: 0.8966 (t) cc_final: 0.8495 (p) REVERT: A 1556 ASN cc_start: 0.8377 (t0) cc_final: 0.8144 (t0) REVERT: A 1613 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 1827 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: A 1943 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7869 (mtm110) REVERT: A 2125 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 2211 GLN cc_start: 0.7951 (tp40) cc_final: 0.7696 (tp40) REVERT: A 2214 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7199 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (tt) REVERT: B 989 ARG cc_start: 0.8444 (ttp-170) cc_final: 0.8029 (ttp80) REVERT: B 1068 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8295 (mmtp) REVERT: B 1080 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8759 (mm-30) REVERT: B 1207 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8426 (ttpp) REVERT: B 1302 GLN cc_start: 0.8651 (tp40) cc_final: 0.8134 (tp40) REVERT: B 1304 MET cc_start: 0.8346 (ttt) cc_final: 0.7449 (ttt) REVERT: B 1326 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8310 (mt-10) REVERT: B 1340 GLN cc_start: 0.7997 (mm110) cc_final: 0.7637 (mm110) REVERT: B 1343 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7063 (m) REVERT: B 1511 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7831 (t-170) REVERT: B 1906 LYS cc_start: 0.8854 (mtmp) cc_final: 0.8509 (mttp) REVERT: B 1995 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 2101 MET cc_start: 0.9140 (mmt) cc_final: 0.8905 (mmt) outliers start: 46 outliers final: 32 residues processed: 283 average time/residue: 0.4096 time to fit residues: 174.6342 Evaluate side-chains 284 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1578 ASN Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2125 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1511 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2194 LEU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 185 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1380 ASN B1501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082606 restraints weight = 101860.888| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.00 r_work: 0.2818 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22169 Z= 0.138 Angle : 0.521 5.402 30026 Z= 0.267 Chirality : 0.040 0.139 3347 Planarity : 0.004 0.047 3861 Dihedral : 8.014 177.589 3024 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.00 % Allowed : 21.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.45 (0.16), residues: 2734 helix: 0.88 (0.17), residues: 976 sheet: -1.27 (0.23), residues: 482 loop : -0.75 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1437 TYR 0.026 0.001 TYR A1018 PHE 0.013 0.001 PHE A2171 TRP 0.011 0.001 TRP B 921 HIS 0.004 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (22167) covalent geometry : angle 0.52109 / 0.27 (30026) hydrogen bonds : bond 0.03636 / 2.46 ( 865) hydrogen bonds : angle 4.62474 / 3.25 ( 2540) Misc. bond : bond 0.00006 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8651 (t0) cc_final: 0.8295 (t0) REVERT: A 1178 GLN cc_start: 0.7295 (mm-40) cc_final: 0.7026 (mm-40) REVERT: A 1252 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 1258 TYR cc_start: 0.7993 (t80) cc_final: 0.7673 (t80) REVERT: A 1262 LEU cc_start: 0.8573 (mt) cc_final: 0.8153 (mp) REVERT: A 1293 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 1313 ARG cc_start: 0.8537 (mmt180) cc_final: 0.8322 (mmt90) REVERT: A 1510 SER cc_start: 0.8973 (t) cc_final: 0.8539 (p) REVERT: A 1556 ASN cc_start: 0.8303 (t0) cc_final: 0.8067 (t0) REVERT: A 1613 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 1827 ASP cc_start: 0.8662 (m-30) cc_final: 0.8424 (m-30) REVERT: A 1848 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8382 (mtmt) REVERT: A 1943 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7836 (mtm110) REVERT: A 2125 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 2167 TYR cc_start: 0.8427 (t80) cc_final: 0.7984 (t80) REVERT: A 2181 MET cc_start: 0.8923 (mtt) cc_final: 0.8404 (mtt) REVERT: A 2211 GLN cc_start: 0.8273 (tp40) cc_final: 0.7968 (tp40) REVERT: A 2214 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7203 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 989 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8153 (ttp80) REVERT: B 1068 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8374 (mmtp) REVERT: B 1080 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8782 (mm-30) REVERT: B 1178 GLN cc_start: 0.5594 (tt0) cc_final: 0.5081 (tt0) REVERT: B 1207 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8490 (ttpp) REVERT: B 1302 GLN cc_start: 0.8694 (tp40) cc_final: 0.8223 (tp40) REVERT: B 1304 MET cc_start: 0.8425 (ttt) cc_final: 0.7441 (ttt) REVERT: B 1326 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8287 (mt-10) REVERT: B 1343 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7146 (m) REVERT: B 1906 LYS cc_start: 0.8875 (mtmp) cc_final: 0.8551 (mttp) REVERT: B 1995 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 2101 MET cc_start: 0.9076 (mmt) cc_final: 0.8821 (mmt) outliers start: 47 outliers final: 32 residues processed: 275 average time/residue: 0.4174 time to fit residues: 172.7192 Evaluate side-chains 275 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1848 LYS Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2125 GLU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 127 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.081777 restraints weight = 101253.120| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.05 r_work: 0.2810 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22169 Z= 0.153 Angle : 0.525 5.522 30026 Z= 0.270 Chirality : 0.040 0.141 3347 Planarity : 0.004 0.048 3861 Dihedral : 7.619 179.765 3024 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 2.13 % Allowed : 21.31 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.44 (0.16), residues: 2734 helix: 0.90 (0.17), residues: 977 sheet: -1.29 (0.23), residues: 474 loop : -0.74 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1818 TYR 0.026 0.001 TYR A1018 PHE 0.014 0.001 PHE A2171 TRP 0.010 0.001 TRP B 921 HIS 0.004 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (22167) covalent geometry : angle 0.52547 / 0.27 (30026) hydrogen bonds : bond 0.03660 / 2.48 ( 865) hydrogen bonds : angle 4.59180 / 3.23 ( 2540) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8665 (t0) cc_final: 0.8317 (t0) REVERT: A 1178 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6888 (mm-40) REVERT: A 1252 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 1258 TYR cc_start: 0.8016 (t80) cc_final: 0.7654 (t80) REVERT: A 1262 LEU cc_start: 0.8513 (mt) cc_final: 0.8079 (mp) REVERT: A 1293 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 1313 ARG cc_start: 0.8561 (mmt180) cc_final: 0.8336 (mmt90) REVERT: A 1510 SER cc_start: 0.8969 (t) cc_final: 0.8526 (p) REVERT: A 1556 ASN cc_start: 0.8321 (t0) cc_final: 0.8086 (t0) REVERT: A 1613 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8589 (p) REVERT: A 1827 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: A 1848 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8380 (mtmt) REVERT: A 2167 TYR cc_start: 0.8570 (t80) cc_final: 0.8160 (t80) REVERT: A 2181 MET cc_start: 0.8954 (mtt) cc_final: 0.8453 (mtt) REVERT: A 2214 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7195 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 989 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8072 (ttt180) REVERT: B 1068 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8351 (mmtp) REVERT: B 1080 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8843 (mm-30) REVERT: B 1207 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8500 (ttpp) REVERT: B 1302 GLN cc_start: 0.8722 (tp40) cc_final: 0.8215 (tp40) REVERT: B 1304 MET cc_start: 0.8491 (ttt) cc_final: 0.7478 (ttt) REVERT: B 1340 GLN cc_start: 0.8123 (mm110) cc_final: 0.7793 (mm110) REVERT: B 1343 VAL cc_start: 0.7407 (OUTLIER) cc_final: 0.7116 (m) REVERT: B 1906 LYS cc_start: 0.8890 (mtmp) cc_final: 0.8520 (mttp) REVERT: B 1995 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8610 (mt) outliers start: 50 outliers final: 37 residues processed: 274 average time/residue: 0.4394 time to fit residues: 182.2687 Evaluate side-chains 284 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1848 LYS Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1183 TRP Chi-restraints excluded: chain B residue 1294 THR Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1977 MET Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2015 GLN Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082291 restraints weight = 107212.398| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.11 r_work: 0.2819 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22169 Z= 0.117 Angle : 0.508 5.604 30026 Z= 0.261 Chirality : 0.040 0.195 3347 Planarity : 0.004 0.061 3861 Dihedral : 7.440 179.061 3021 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 21.40 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.36 (0.16), residues: 2734 helix: 0.98 (0.17), residues: 976 sheet: -1.28 (0.22), residues: 481 loop : -0.69 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1943 TYR 0.023 0.001 TYR A1018 PHE 0.018 0.001 PHE A1417 TRP 0.011 0.001 TRP A1889 HIS 0.003 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22167) covalent geometry : angle 0.50845 / 0.26 (30026) hydrogen bonds : bond 0.03432 / 2.32 ( 865) hydrogen bonds : angle 4.51093 / 3.17 ( 2540) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8649 (t0) cc_final: 0.8289 (t0) REVERT: A 1178 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6865 (mm-40) REVERT: A 1313 ARG cc_start: 0.8532 (mmt180) cc_final: 0.8304 (mmt90) REVERT: A 1439 MET cc_start: 0.9101 (mpt) cc_final: 0.8666 (mpt) REVERT: A 1510 SER cc_start: 0.8993 (t) cc_final: 0.8542 (p) REVERT: A 1556 ASN cc_start: 0.8280 (t0) cc_final: 0.8039 (t0) REVERT: A 1613 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8608 (p) REVERT: A 1827 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8393 (m-30) REVERT: A 1848 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8391 (mtmt) REVERT: A 1943 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7918 (mtm110) REVERT: A 2167 TYR cc_start: 0.8558 (t80) cc_final: 0.8141 (t80) REVERT: A 2181 MET cc_start: 0.8944 (mtt) cc_final: 0.8452 (mtt) REVERT: A 2214 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7192 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 989 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8067 (ttt180) REVERT: B 1068 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8304 (mmtp) REVERT: B 1080 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8874 (mm-30) REVERT: B 1207 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8497 (ttpp) REVERT: B 1302 GLN cc_start: 0.8727 (tp40) cc_final: 0.8232 (tp40) REVERT: B 1304 MET cc_start: 0.8484 (ttt) cc_final: 0.7461 (ttt) REVERT: B 1340 GLN cc_start: 0.8133 (mm110) cc_final: 0.7834 (mm110) REVERT: B 1343 VAL cc_start: 0.7347 (OUTLIER) cc_final: 0.7055 (m) REVERT: B 1906 LYS cc_start: 0.8885 (mtmp) cc_final: 0.8510 (mttp) REVERT: B 1995 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8608 (mt) outliers start: 45 outliers final: 35 residues processed: 266 average time/residue: 0.4369 time to fit residues: 174.6018 Evaluate side-chains 278 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1239 ASN Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1422 ILE Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1848 LYS Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1183 TRP Chi-restraints excluded: chain B residue 1294 THR Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1977 MET Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2015 GLN Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 168 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1190 ASN B1511 HIS B1642 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.079890 restraints weight = 103615.365| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.06 r_work: 0.2780 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22169 Z= 0.227 Angle : 0.562 5.925 30026 Z= 0.290 Chirality : 0.042 0.165 3347 Planarity : 0.005 0.048 3861 Dihedral : 7.610 179.859 3021 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 2.09 % Allowed : 21.18 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.52 (0.16), residues: 2734 helix: 0.84 (0.17), residues: 975 sheet: -1.29 (0.23), residues: 475 loop : -0.81 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1943 TYR 0.030 0.002 TYR A1018 PHE 0.019 0.001 PHE A1417 TRP 0.013 0.001 TRP B 921 HIS 0.005 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (22167) covalent geometry : angle 0.56183 / 0.29 (30026) hydrogen bonds : bond 0.03945 / 2.65 ( 865) hydrogen bonds : angle 4.63871 / 3.27 ( 2540) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8630 (t0) cc_final: 0.8271 (t0) REVERT: A 1252 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 1293 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 1313 ARG cc_start: 0.8568 (mmt180) cc_final: 0.8353 (mmt90) REVERT: A 1510 SER cc_start: 0.9009 (t) cc_final: 0.8583 (p) REVERT: A 1556 ASN cc_start: 0.8273 (t0) cc_final: 0.8054 (t0) REVERT: A 1613 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 1827 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: A 1848 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8444 (mtmt) REVERT: A 1943 ARG cc_start: 0.8216 (mtp-110) cc_final: 0.7912 (mtm110) REVERT: A 2167 TYR cc_start: 0.8556 (t80) cc_final: 0.8153 (t80) REVERT: A 2181 MET cc_start: 0.8978 (mtt) cc_final: 0.8503 (mtt) REVERT: A 2214 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7258 (ttp-110) REVERT: A 2257 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8353 (tt) REVERT: B 989 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.8075 (ttt180) REVERT: B 1068 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8377 (mmtp) REVERT: B 1080 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8863 (mm-30) REVERT: B 1207 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8467 (ttpp) REVERT: B 1302 GLN cc_start: 0.8766 (tp40) cc_final: 0.8268 (tp40) REVERT: B 1343 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7097 (m) REVERT: B 1381 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (mp) REVERT: B 1471 MET cc_start: 0.8702 (ttm) cc_final: 0.8201 (ttp) REVERT: B 1595 ASP cc_start: 0.7704 (m-30) cc_final: 0.7486 (t0) REVERT: B 1906 LYS cc_start: 0.8927 (mtmp) cc_final: 0.8543 (mttp) REVERT: B 1995 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8661 (mt) outliers start: 49 outliers final: 33 residues processed: 269 average time/residue: 0.4364 time to fit residues: 175.4612 Evaluate side-chains 272 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1848 LYS Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1172 CYS Chi-restraints excluded: chain B residue 1183 TRP Chi-restraints excluded: chain B residue 1294 THR Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1404 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1977 MET Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2015 GLN Chi-restraints excluded: chain B residue 2194 LEU Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 chunk 194 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1511 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082228 restraints weight = 111153.403| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.14 r_work: 0.2812 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22169 Z= 0.105 Angle : 0.508 5.300 30026 Z= 0.261 Chirality : 0.040 0.137 3347 Planarity : 0.004 0.054 3861 Dihedral : 7.413 179.182 3021 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.71 % Allowed : 21.61 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.32 (0.16), residues: 2734 helix: 1.03 (0.17), residues: 977 sheet: -1.29 (0.22), residues: 483 loop : -0.66 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1943 TYR 0.022 0.001 TYR A1018 PHE 0.015 0.001 PHE B1173 TRP 0.013 0.001 TRP A1889 HIS 0.003 0.001 HIS A1135 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 (22167) covalent geometry : angle 0.50825 / 0.26 (30026) hydrogen bonds : bond 0.03349 / 2.25 ( 865) hydrogen bonds : angle 4.47882 / 3.16 ( 2540) Misc. bond : bond 0.00018 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2241 is missing expected H atoms. Skipping. Residue SER 2241 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 898 ASN cc_start: 0.8608 (t0) cc_final: 0.8252 (t0) REVERT: A 1293 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 1313 ARG cc_start: 0.8518 (mmt180) cc_final: 0.8297 (mmt90) REVERT: A 1510 SER cc_start: 0.9028 (t) cc_final: 0.8616 (p) REVERT: A 1556 ASN cc_start: 0.8229 (t0) cc_final: 0.8009 (t0) REVERT: A 1613 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 1827 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: A 1848 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8453 (mtmt) REVERT: A 1943 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7904 (mtm110) REVERT: A 2167 TYR cc_start: 0.8542 (t80) cc_final: 0.8135 (t80) REVERT: A 2181 MET cc_start: 0.8944 (mtt) cc_final: 0.8459 (mtt) REVERT: A 2214 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7225 (ttp-110) REVERT: A 2253 ARG cc_start: 0.6602 (ttp-110) cc_final: 0.6067 (ttm-80) REVERT: A 2257 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8401 (tt) REVERT: B 989 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.8103 (ttt180) REVERT: B 1068 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8333 (mmtp) REVERT: B 1080 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8882 (mm-30) REVERT: B 1207 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8451 (ttpp) REVERT: B 1302 GLN cc_start: 0.8762 (tp40) cc_final: 0.8278 (tp40) REVERT: B 1304 MET cc_start: 0.8522 (ttt) cc_final: 0.7424 (ttt) REVERT: B 1340 GLN cc_start: 0.8382 (mm110) cc_final: 0.8120 (mm110) REVERT: B 1343 VAL cc_start: 0.7327 (OUTLIER) cc_final: 0.7042 (m) REVERT: B 1381 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8725 (mp) REVERT: B 1906 LYS cc_start: 0.8906 (mtmp) cc_final: 0.8523 (mttp) REVERT: B 1995 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8622 (mt) outliers start: 40 outliers final: 28 residues processed: 259 average time/residue: 0.4285 time to fit residues: 164.6567 Evaluate side-chains 266 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1443 TYR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1602 ARG Chi-restraints excluded: chain A residue 1613 SER Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1658 LEU Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1775 SER Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1848 LYS Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 2025 LEU Chi-restraints excluded: chain A residue 2029 THR Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2194 LEU Chi-restraints excluded: chain A residue 2257 LEU Chi-restraints excluded: chain B residue 887 ILE Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1183 TRP Chi-restraints excluded: chain B residue 1294 THR Chi-restraints excluded: chain B residue 1343 VAL Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1455 HIS Chi-restraints excluded: chain B residue 1775 SER Chi-restraints excluded: chain B residue 1961 CYS Chi-restraints excluded: chain B residue 1977 MET Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2015 GLN Chi-restraints excluded: chain B residue 2251 LEU Chi-restraints excluded: chain B residue 2267 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 125 optimal weight: 0.0870 chunk 164 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.081904 restraints weight = 110397.996| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.13 r_work: 0.2811 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22169 Z= 0.120 Angle : 0.508 5.350 30026 Z= 0.260 Chirality : 0.040 0.140 3347 Planarity : 0.004 0.050 3861 Dihedral : 7.317 177.973 3019 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.58 % Allowed : 21.65 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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 are not related in a simple way. whole: -0.29 (0.16), residues: 2734 helix: 1.06 (0.17), residues: 976 sheet: -1.28 (0.22), residues: 481 loop : -0.66 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1943 TYR 0.024 0.001 TYR A1018 PHE 0.014 0.001 PHE B2171 TRP 0.011 0.001 TRP B1889 HIS 0.003 0.001 HIS A 903 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (22167) covalent geometry : angle 0.50823 / 0.26 (30026) hydrogen bonds : bond 0.03311 / 2.22 ( 865) hydrogen bonds : angle 4.43355 / 3.12 ( 2540) Misc. bond : bond 0.00006 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12475.01 seconds wall clock time: 212 minutes 0.40 seconds (12720.40 seconds total)