Starting phenix.real_space_refine on Sat Feb 7 15:24:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zit_74283/02_2026/9zit_74283.map" } resolution = 3.1 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= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 201 5.16 5 C 21681 2.51 5 N 5442 2.21 5 O 5763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33087 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1359, 11029 Classifications: {'peptide': 1359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1303} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Restraints were copied for chains: B, C Time building chain proxies: 14.65, per 1000 atoms: 0.44 Number of scatterers: 33087 At special positions: 0 Unit cell: (198.72, 197.64, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 201 16.00 O 5763 8.00 N 5442 7.00 C 21681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1273 " distance=2.37 Simple disulfide: pdb=" SG CYS B1246 " - pdb=" SG CYS B1273 " distance=2.37 Simple disulfide: pdb=" SG CYS C1246 " - pdb=" SG CYS C1273 " distance=2.37 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7752 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 9 sheets defined 67.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 801 through 830 removed outlier: 3.534A pdb=" N ILE A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 846 Processing helix chain 'A' and resid 849 through 863 removed outlier: 4.115A pdb=" N LEU A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 887 removed outlier: 4.743A pdb=" N LEU A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A 880 " --> pdb=" O CYS A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 962 removed outlier: 4.083A pdb=" N ALA A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 960 " --> pdb=" O ARG A 956 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 961 " --> pdb=" O HIS A 957 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 981 removed outlier: 3.619A pdb=" N HIS A 978 " --> pdb=" O PRO A 974 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 981 " --> pdb=" O HIS A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 995 Processing helix chain 'A' and resid 998 through 1017 removed outlier: 3.678A pdb=" N LEU A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1034 removed outlier: 4.185A pdb=" N ILE A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1062 Proline residue: A1055 - end of helix Processing helix chain 'A' and resid 1073 through 1078 removed outlier: 3.804A pdb=" N TRP A1077 " --> pdb=" O PRO A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 Processing helix chain 'A' and resid 1103 through 1127 removed outlier: 3.578A pdb=" N LEU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1140 Processing helix chain 'A' and resid 1159 through 1170 Processing helix chain 'A' and resid 1172 through 1185 removed outlier: 3.870A pdb=" N MET A1176 " --> pdb=" O TRP A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1209 removed outlier: 3.804A pdb=" N GLY A1192 " --> pdb=" O LEU A1188 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A1193 " --> pdb=" O PHE A1189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A1198 " --> pdb=" O ILE A1194 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1247 removed outlier: 3.884A pdb=" N TYR A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A1231 " --> pdb=" O LEU A1227 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1269 removed outlier: 3.517A pdb=" N LEU A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1292 Processing helix chain 'A' and resid 1302 through 1315 Processing helix chain 'A' and resid 1321 through 1337 removed outlier: 3.513A pdb=" N MET A1326 " --> pdb=" O PHE A1322 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A1328 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A1337 " --> pdb=" O VAL A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1385 removed outlier: 3.579A pdb=" N LEU A1342 " --> pdb=" O ARG A1338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A1380 " --> pdb=" O TYR A1376 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A1381 " --> pdb=" O GLN A1377 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A1383 " --> pdb=" O GLN A1379 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1407 removed outlier: 3.841A pdb=" N MET A1405 " --> pdb=" O ASP A1402 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A1407 " --> pdb=" O TYR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1578 Proline residue: A1571 - end of helix Processing helix chain 'A' and resid 1581 through 1594 removed outlier: 4.403A pdb=" N THR A1587 " --> pdb=" O GLU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1613 removed outlier: 4.046A pdb=" N ASN A1604 " --> pdb=" O THR A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1630 removed outlier: 3.765A pdb=" N LEU A1617 " --> pdb=" O HIS A1613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1618 " --> pdb=" O THR A1614 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A1619 " --> pdb=" O ASP A1615 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1646 removed outlier: 3.709A pdb=" N LEU A1639 " --> pdb=" O LEU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1675 Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1717 through 1737 Processing helix chain 'A' and resid 1813 through 1821 Processing helix chain 'A' and resid 1831 through 1849 removed outlier: 3.868A pdb=" N MET A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1872 through 1893 removed outlier: 4.546A pdb=" N VAL A1876 " --> pdb=" O VAL A1872 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A1877 " --> pdb=" O THR A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1918 Processing helix chain 'A' and resid 1918 through 1924 Processing helix chain 'A' and resid 1930 through 1953 removed outlier: 3.791A pdb=" N ALA A1935 " --> pdb=" O HIS A1931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A1943 " --> pdb=" O ILE A1939 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1946 " --> pdb=" O CYS A1942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1982 Processing helix chain 'A' and resid 1985 through 1996 Processing helix chain 'A' and resid 2002 through 2029 removed outlier: 3.515A pdb=" N PHE A2006 " --> pdb=" O PRO A2002 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A2029 " --> pdb=" O PHE A2025 " (cutoff:3.500A) Processing helix chain 'A' and resid 2038 through 2069 removed outlier: 3.894A pdb=" N PHE A2047 " --> pdb=" O TYR A2043 " (cutoff:3.500A) Proline residue: A2048 - end of helix Proline residue: A2060 - end of helix removed outlier: 4.347A pdb=" N GLN A2069 " --> pdb=" O SER A2065 " (cutoff:3.500A) Processing helix chain 'A' and resid 2110 through 2123 removed outlier: 3.559A pdb=" N THR A2122 " --> pdb=" O ASN A2118 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A2123 " --> pdb=" O GLN A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2144 removed outlier: 3.730A pdb=" N ILE A2133 " --> pdb=" O ASP A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2145 through 2146 No H-bonds generated for 'chain 'A' and resid 2145 through 2146' Processing helix chain 'A' and resid 2147 through 2149 No H-bonds generated for 'chain 'A' and resid 2147 through 2149' Processing helix chain 'A' and resid 2167 through 2180 removed outlier: 3.521A pdb=" N ARG A2180 " --> pdb=" O ASP A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2217 through 2230 Processing helix chain 'A' and resid 2258 through 2267 removed outlier: 3.591A pdb=" N THR A2263 " --> pdb=" O SER A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2283 removed outlier: 3.926A pdb=" N ALA A2283 " --> pdb=" O LYS A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2351 Processing helix chain 'A' and resid 2352 through 2371 Processing helix chain 'A' and resid 2371 through 2377 Processing helix chain 'A' and resid 2379 through 2384 removed outlier: 3.581A pdb=" N VAL A2383 " --> pdb=" O PRO A2380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A2384 " --> pdb=" O SER A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2407 removed outlier: 3.620A pdb=" N CYS A2398 " --> pdb=" O LEU A2394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A2406 " --> pdb=" O TYR A2402 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A2407 " --> pdb=" O LEU A2403 " (cutoff:3.500A) Processing helix chain 'A' and resid 2409 through 2424 removed outlier: 3.523A pdb=" N GLN A2414 " --> pdb=" O PHE A2410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A2417 " --> pdb=" O GLU A2413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A2423 " --> pdb=" O LYS A2419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A2424 " --> pdb=" O LEU A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2435 Processing helix chain 'A' and resid 2437 through 2442 Processing helix chain 'B' and resid 802 through 830 removed outlier: 3.533A pdb=" N ILE B 830 " --> pdb=" O PHE B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 Processing helix chain 'B' and resid 849 through 863 removed outlier: 4.115A pdb=" N LEU B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 887 removed outlier: 4.744A pdb=" N LEU B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE B 880 " --> pdb=" O CYS B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 962 removed outlier: 4.083A pdb=" N ALA B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 960 " --> pdb=" O ARG B 956 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 961 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 981 removed outlier: 3.619A pdb=" N HIS B 978 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 981 " --> pdb=" O HIS B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 995 Processing helix chain 'B' and resid 998 through 1017 removed outlier: 3.678A pdb=" N LEU B1002 " --> pdb=" O TYR B 998 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1034 removed outlier: 4.185A pdb=" N ILE B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B1034 " --> pdb=" O LEU B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1062 Proline residue: B1055 - end of helix Processing helix chain 'B' and resid 1073 through 1078 removed outlier: 3.805A pdb=" N TRP B1077 " --> pdb=" O PRO B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1094 Processing helix chain 'B' and resid 1103 through 1127 removed outlier: 3.578A pdb=" N LEU B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B1126 " --> pdb=" O ALA B1122 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B1127 " --> pdb=" O VAL B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1140 Processing helix chain 'B' and resid 1159 through 1170 Processing helix chain 'B' and resid 1172 through 1185 removed outlier: 3.870A pdb=" N MET B1176 " --> pdb=" O TRP B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1209 removed outlier: 3.804A pdb=" N GLY B1192 " --> pdb=" O LEU B1188 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B1193 " --> pdb=" O PHE B1189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B1198 " --> pdb=" O ILE B1194 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR B1199 " --> pdb=" O ILE B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1215 through 1247 removed outlier: 3.884A pdb=" N TYR B1230 " --> pdb=" O ALA B1226 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B1231 " --> pdb=" O LEU B1227 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B1239 " --> pdb=" O ILE B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1269 removed outlier: 3.517A pdb=" N LEU B1268 " --> pdb=" O ILE B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1292 Processing helix chain 'B' and resid 1302 through 1315 Processing helix chain 'B' and resid 1321 through 1337 removed outlier: 3.513A pdb=" N MET B1326 " --> pdb=" O PHE B1322 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B1328 " --> pdb=" O HIS B1324 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B1337 " --> pdb=" O VAL B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1385 removed outlier: 3.579A pdb=" N LEU B1342 " --> pdb=" O ARG B1338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B1380 " --> pdb=" O TYR B1376 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B1381 " --> pdb=" O GLN B1377 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B1383 " --> pdb=" O GLN B1379 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B1384 " --> pdb=" O ILE B1380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B1385 " --> pdb=" O GLU B1381 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1407 removed outlier: 3.841A pdb=" N MET B1405 " --> pdb=" O ASP B1402 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS B1407 " --> pdb=" O TYR B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1559 through 1578 Proline residue: B1571 - end of helix Processing helix chain 'B' and resid 1581 through 1594 removed outlier: 4.403A pdb=" N THR B1587 " --> pdb=" O GLU B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1600 through 1613 removed outlier: 4.046A pdb=" N ASN B1604 " --> pdb=" O THR B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1613 through 1630 removed outlier: 3.764A pdb=" N LEU B1617 " --> pdb=" O HIS B1613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B1618 " --> pdb=" O THR B1614 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B1619 " --> pdb=" O ASP B1615 " (cutoff:3.500A) Processing helix chain 'B' and resid 1635 through 1646 removed outlier: 3.709A pdb=" N LEU B1639 " --> pdb=" O LEU B1635 " (cutoff:3.500A) Processing helix chain 'B' and resid 1655 through 1675 Processing helix chain 'B' and resid 1685 through 1690 Processing helix chain 'B' and resid 1717 through 1737 Processing helix chain 'B' and resid 1813 through 1821 Processing helix chain 'B' and resid 1831 through 1849 removed outlier: 3.868A pdb=" N MET B1835 " --> pdb=" O LEU B1831 " (cutoff:3.500A) Processing helix chain 'B' and resid 1872 through 1893 removed outlier: 4.546A pdb=" N VAL B1876 " --> pdb=" O VAL B1872 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B1877 " --> pdb=" O THR B1873 " (cutoff:3.500A) Processing helix chain 'B' and resid 1897 through 1918 Processing helix chain 'B' and resid 1918 through 1924 Processing helix chain 'B' and resid 1930 through 1953 removed outlier: 3.791A pdb=" N ALA B1935 " --> pdb=" O HIS B1931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B1943 " --> pdb=" O ILE B1939 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B1946 " --> pdb=" O CYS B1942 " (cutoff:3.500A) Processing helix chain 'B' and resid 1969 through 1982 Processing helix chain 'B' and resid 1985 through 1996 Processing helix chain 'B' and resid 2002 through 2029 removed outlier: 3.516A pdb=" N PHE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B2029 " --> pdb=" O PHE B2025 " (cutoff:3.500A) Processing helix chain 'B' and resid 2038 through 2069 removed outlier: 3.893A pdb=" N PHE B2047 " --> pdb=" O TYR B2043 " (cutoff:3.500A) Proline residue: B2048 - end of helix Proline residue: B2060 - end of helix removed outlier: 4.347A pdb=" N GLN B2069 " --> pdb=" O SER B2065 " (cutoff:3.500A) Processing helix chain 'B' and resid 2110 through 2123 removed outlier: 3.560A pdb=" N THR B2122 " --> pdb=" O ASN B2118 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B2123 " --> pdb=" O GLN B2119 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2144 removed outlier: 3.730A pdb=" N ILE B2133 " --> pdb=" O ASP B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2145 through 2146 No H-bonds generated for 'chain 'B' and resid 2145 through 2146' Processing helix chain 'B' and resid 2147 through 2149 No H-bonds generated for 'chain 'B' and resid 2147 through 2149' Processing helix chain 'B' and resid 2167 through 2180 removed outlier: 3.521A pdb=" N ARG B2180 " --> pdb=" O ASP B2176 " (cutoff:3.500A) Processing helix chain 'B' and resid 2217 through 2230 Processing helix chain 'B' and resid 2258 through 2267 removed outlier: 3.591A pdb=" N THR B2263 " --> pdb=" O SER B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2278 through 2283 removed outlier: 3.926A pdb=" N ALA B2283 " --> pdb=" O LYS B2279 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2351 Processing helix chain 'B' and resid 2352 through 2371 Processing helix chain 'B' and resid 2371 through 2377 Processing helix chain 'B' and resid 2379 through 2384 removed outlier: 3.581A pdb=" N VAL B2383 " --> pdb=" O PRO B2380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B2384 " --> pdb=" O SER B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2407 removed outlier: 3.621A pdb=" N CYS B2398 " --> pdb=" O LEU B2394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B2406 " --> pdb=" O TYR B2402 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B2407 " --> pdb=" O LEU B2403 " (cutoff:3.500A) Processing helix chain 'B' and resid 2409 through 2424 removed outlier: 3.523A pdb=" N GLN B2414 " --> pdb=" O PHE B2410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B2417 " --> pdb=" O GLU B2413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B2423 " --> pdb=" O LYS B2419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B2424 " --> pdb=" O LEU B2420 " (cutoff:3.500A) Processing helix chain 'B' and resid 2426 through 2435 Processing helix chain 'B' and resid 2437 through 2442 Processing helix chain 'C' and resid 802 through 830 removed outlier: 3.534A pdb=" N ILE C 830 " --> pdb=" O PHE C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 Processing helix chain 'C' and resid 849 through 863 removed outlier: 4.115A pdb=" N LEU C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 857 " --> pdb=" O LEU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 887 removed outlier: 4.743A pdb=" N LEU C 879 " --> pdb=" O MET C 875 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE C 880 " --> pdb=" O CYS C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 962 removed outlier: 4.083A pdb=" N ALA C 946 " --> pdb=" O ILE C 942 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 960 " --> pdb=" O ARG C 956 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 961 " --> pdb=" O HIS C 957 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 981 removed outlier: 3.619A pdb=" N HIS C 978 " --> pdb=" O PRO C 974 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 981 " --> pdb=" O HIS C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 995 Processing helix chain 'C' and resid 998 through 1017 removed outlier: 3.678A pdb=" N LEU C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C1003 " --> pdb=" O LYS C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1034 removed outlier: 4.186A pdb=" N ILE C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C1034 " --> pdb=" O LEU C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1062 Proline residue: C1055 - end of helix Processing helix chain 'C' and resid 1073 through 1078 removed outlier: 3.804A pdb=" N TRP C1077 " --> pdb=" O PRO C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1094 Processing helix chain 'C' and resid 1103 through 1127 removed outlier: 3.578A pdb=" N LEU C1107 " --> pdb=" O PRO C1103 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C1126 " --> pdb=" O ALA C1122 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C1127 " --> pdb=" O VAL C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1140 Processing helix chain 'C' and resid 1159 through 1170 Processing helix chain 'C' and resid 1172 through 1185 removed outlier: 3.870A pdb=" N MET C1176 " --> pdb=" O TRP C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1208 removed outlier: 3.804A pdb=" N GLY C1192 " --> pdb=" O LEU C1188 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C1193 " --> pdb=" O PHE C1189 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C1198 " --> pdb=" O ILE C1194 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR C1199 " --> pdb=" O ILE C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1247 removed outlier: 3.884A pdb=" N TYR C1230 " --> pdb=" O ALA C1226 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR C1231 " --> pdb=" O LEU C1227 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C1239 " --> pdb=" O ILE C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1256 through 1269 removed outlier: 3.517A pdb=" N LEU C1268 " --> pdb=" O ILE C1264 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1292 Processing helix chain 'C' and resid 1302 through 1315 Processing helix chain 'C' and resid 1321 through 1337 removed outlier: 3.513A pdb=" N MET C1326 " --> pdb=" O PHE C1322 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL C1327 " --> pdb=" O GLN C1323 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C1328 " --> pdb=" O HIS C1324 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN C1337 " --> pdb=" O VAL C1333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1385 removed outlier: 3.579A pdb=" N LEU C1342 " --> pdb=" O ARG C1338 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C1380 " --> pdb=" O TYR C1376 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C1381 " --> pdb=" O GLN C1377 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C1383 " --> pdb=" O GLN C1379 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C1384 " --> pdb=" O ILE C1380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C1385 " --> pdb=" O GLU C1381 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1407 removed outlier: 3.841A pdb=" N MET C1405 " --> pdb=" O ASP C1402 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS C1407 " --> pdb=" O TYR C1404 " (cutoff:3.500A) Processing helix chain 'C' and resid 1559 through 1578 Proline residue: C1571 - end of helix Processing helix chain 'C' and resid 1581 through 1594 removed outlier: 4.403A pdb=" N THR C1587 " --> pdb=" O GLU C1583 " (cutoff:3.500A) Processing helix chain 'C' and resid 1600 through 1613 removed outlier: 4.046A pdb=" N ASN C1604 " --> pdb=" O THR C1600 " (cutoff:3.500A) Processing helix chain 'C' and resid 1613 through 1630 removed outlier: 3.764A pdb=" N LEU C1617 " --> pdb=" O HIS C1613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C1618 " --> pdb=" O THR C1614 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C1619 " --> pdb=" O ASP C1615 " (cutoff:3.500A) Processing helix chain 'C' and resid 1635 through 1646 removed outlier: 3.709A pdb=" N LEU C1639 " --> pdb=" O LEU C1635 " (cutoff:3.500A) Processing helix chain 'C' and resid 1655 through 1675 Processing helix chain 'C' and resid 1685 through 1690 Processing helix chain 'C' and resid 1717 through 1737 Processing helix chain 'C' and resid 1813 through 1821 Processing helix chain 'C' and resid 1831 through 1849 removed outlier: 3.868A pdb=" N MET C1835 " --> pdb=" O LEU C1831 " (cutoff:3.500A) Processing helix chain 'C' and resid 1872 through 1893 removed outlier: 4.546A pdb=" N VAL C1876 " --> pdb=" O VAL C1872 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C1877 " --> pdb=" O THR C1873 " (cutoff:3.500A) Processing helix chain 'C' and resid 1897 through 1918 Processing helix chain 'C' and resid 1918 through 1924 Processing helix chain 'C' and resid 1930 through 1953 removed outlier: 3.791A pdb=" N ALA C1935 " --> pdb=" O HIS C1931 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C1943 " --> pdb=" O ILE C1939 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C1946 " --> pdb=" O CYS C1942 " (cutoff:3.500A) Processing helix chain 'C' and resid 1969 through 1982 Processing helix chain 'C' and resid 1985 through 1996 Processing helix chain 'C' and resid 2002 through 2029 removed outlier: 3.515A pdb=" N PHE C2006 " --> pdb=" O PRO C2002 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR C2029 " --> pdb=" O PHE C2025 " (cutoff:3.500A) Processing helix chain 'C' and resid 2038 through 2069 removed outlier: 3.893A pdb=" N PHE C2047 " --> pdb=" O TYR C2043 " (cutoff:3.500A) Proline residue: C2048 - end of helix Proline residue: C2060 - end of helix removed outlier: 4.347A pdb=" N GLN C2069 " --> pdb=" O SER C2065 " (cutoff:3.500A) Processing helix chain 'C' and resid 2110 through 2123 removed outlier: 3.559A pdb=" N THR C2122 " --> pdb=" O ASN C2118 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP C2123 " --> pdb=" O GLN C2119 " (cutoff:3.500A) Processing helix chain 'C' and resid 2129 through 2144 removed outlier: 3.729A pdb=" N ILE C2133 " --> pdb=" O ASP C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2145 through 2146 No H-bonds generated for 'chain 'C' and resid 2145 through 2146' Processing helix chain 'C' and resid 2147 through 2149 No H-bonds generated for 'chain 'C' and resid 2147 through 2149' Processing helix chain 'C' and resid 2167 through 2180 removed outlier: 3.522A pdb=" N ARG C2180 " --> pdb=" O ASP C2176 " (cutoff:3.500A) Processing helix chain 'C' and resid 2217 through 2230 Processing helix chain 'C' and resid 2258 through 2267 removed outlier: 3.591A pdb=" N THR C2263 " --> pdb=" O SER C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2278 through 2283 removed outlier: 3.926A pdb=" N ALA C2283 " --> pdb=" O LYS C2279 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2351 Processing helix chain 'C' and resid 2352 through 2371 Processing helix chain 'C' and resid 2371 through 2377 Processing helix chain 'C' and resid 2379 through 2384 removed outlier: 3.581A pdb=" N VAL C2383 " --> pdb=" O PRO C2380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C2384 " --> pdb=" O SER C2381 " (cutoff:3.500A) Processing helix chain 'C' and resid 2394 through 2407 removed outlier: 3.621A pdb=" N CYS C2398 " --> pdb=" O LEU C2394 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C2406 " --> pdb=" O TYR C2402 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C2407 " --> pdb=" O LEU C2403 " (cutoff:3.500A) Processing helix chain 'C' and resid 2409 through 2424 removed outlier: 3.523A pdb=" N GLN C2414 " --> pdb=" O PHE C2410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C2417 " --> pdb=" O GLU C2413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C2423 " --> pdb=" O LYS C2419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C2424 " --> pdb=" O LEU C2420 " (cutoff:3.500A) Processing helix chain 'C' and resid 2426 through 2435 Processing helix chain 'C' and resid 2437 through 2442 Processing sheet with id=AA1, first strand: chain 'A' and resid 2092 through 2096 removed outlier: 3.659A pdb=" N LYS A2078 " --> pdb=" O THR A2193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2106 through 2107 Processing sheet with id=AA3, first strand: chain 'A' and resid 2236 through 2238 Processing sheet with id=AA4, first strand: chain 'B' and resid 2092 through 2096 removed outlier: 3.658A pdb=" N LYS B2078 " --> pdb=" O THR B2193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2106 through 2107 Processing sheet with id=AA6, first strand: chain 'B' and resid 2236 through 2238 Processing sheet with id=AA7, first strand: chain 'C' and resid 2092 through 2096 removed outlier: 3.659A pdb=" N LYS C2078 " --> pdb=" O THR C2193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2106 through 2107 Processing sheet with id=AA9, first strand: chain 'C' and resid 2236 through 2238 1917 hydrogen bonds defined for protein. 5697 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: 6.01 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5103 1.28 - 1.42: 9403 1.42 - 1.55: 19094 1.55 - 1.69: 18 1.69 - 1.82: 339 Bond restraints: 33957 Sorted by residual: bond pdb=" N PRO A1073 " pdb=" CD PRO A1073 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.05e+02 bond pdb=" N PRO B1073 " pdb=" CD PRO B1073 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" N PRO C1073 " pdb=" CD PRO C1073 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" N PRO A1079 " pdb=" CD PRO A1079 " ideal model delta sigma weight residual 1.473 1.335 0.138 1.40e-02 5.10e+03 9.78e+01 bond pdb=" N PRO B1079 " pdb=" CD PRO B1079 " ideal model delta sigma weight residual 1.473 1.335 0.138 1.40e-02 5.10e+03 9.78e+01 ... (remaining 33952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.16: 45891 6.16 - 12.33: 144 12.33 - 18.49: 15 18.49 - 24.65: 0 24.65 - 30.82: 3 Bond angle restraints: 46053 Sorted by residual: angle pdb=" CA PHE B 841 " pdb=" CB PHE B 841 " pdb=" CG PHE B 841 " ideal model delta sigma weight residual 113.80 123.90 -10.10 1.00e+00 1.00e+00 1.02e+02 angle pdb=" CA PHE A 841 " pdb=" CB PHE A 841 " pdb=" CG PHE A 841 " ideal model delta sigma weight residual 113.80 123.89 -10.09 1.00e+00 1.00e+00 1.02e+02 angle pdb=" CA PHE C 841 " pdb=" CB PHE C 841 " pdb=" CG PHE C 841 " ideal model delta sigma weight residual 113.80 123.87 -10.07 1.00e+00 1.00e+00 1.01e+02 angle pdb=" CA PRO A1073 " pdb=" N PRO A1073 " pdb=" CD PRO A1073 " ideal model delta sigma weight residual 112.00 124.28 -12.28 1.40e+00 5.10e-01 7.69e+01 angle pdb=" CA PRO C1073 " pdb=" N PRO C1073 " pdb=" CD PRO C1073 " ideal model delta sigma weight residual 112.00 124.24 -12.24 1.40e+00 5.10e-01 7.65e+01 ... (remaining 46048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 17309 17.58 - 35.16: 1939 35.16 - 52.73: 567 52.73 - 70.31: 159 70.31 - 87.89: 39 Dihedral angle restraints: 20013 sinusoidal: 8028 harmonic: 11985 Sorted by residual: dihedral pdb=" CD ARG C1373 " pdb=" NE ARG C1373 " pdb=" CZ ARG C1373 " pdb=" NH1 ARG C1373 " ideal model delta sinusoidal sigma weight residual 0.00 63.58 -63.58 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CD ARG A1373 " pdb=" NE ARG A1373 " pdb=" CZ ARG A1373 " pdb=" NH1 ARG A1373 " ideal model delta sinusoidal sigma weight residual 0.00 63.55 -63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CD ARG B1373 " pdb=" NE ARG B1373 " pdb=" CZ ARG B1373 " pdb=" NH1 ARG B1373 " ideal model delta sinusoidal sigma weight residual 0.00 63.53 -63.53 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 20010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4096 0.067 - 0.135: 835 0.135 - 0.202: 168 0.202 - 0.270: 31 0.270 - 0.337: 9 Chirality restraints: 5139 Sorted by residual: chirality pdb=" CG LEU B2348 " pdb=" CB LEU B2348 " pdb=" CD1 LEU B2348 " pdb=" CD2 LEU B2348 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CG LEU A2348 " pdb=" CB LEU A2348 " pdb=" CD1 LEU A2348 " pdb=" CD2 LEU A2348 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CG LEU C2348 " pdb=" CB LEU C2348 " pdb=" CD1 LEU C2348 " pdb=" CD2 LEU C2348 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 5136 not shown) Planarity restraints: 5736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1366 " 0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG A1366 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A1366 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1366 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1366 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1366 " -0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG B1366 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B1366 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B1366 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B1366 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1366 " -0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG C1366 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG C1366 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C1366 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C1366 " -0.025 2.00e-02 2.50e+03 ... (remaining 5733 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 171 2.62 - 3.19: 30751 3.19 - 3.76: 49596 3.76 - 4.33: 66026 4.33 - 4.90: 105732 Nonbonded interactions: 252276 Sorted by model distance: nonbonded pdb=" O ASN B2181 " pdb=" OD1 ASN B2181 " model vdw 2.050 3.040 nonbonded pdb=" O ASN A2181 " pdb=" OD1 ASN A2181 " model vdw 2.050 3.040 nonbonded pdb=" O ASN C2181 " pdb=" OD1 ASN C2181 " model vdw 2.051 3.040 nonbonded pdb=" O GLU B2200 " pdb=" OD1 ASN B2201 " model vdw 2.092 3.040 nonbonded pdb=" O GLU C2200 " pdb=" OD1 ASN C2201 " model vdw 2.092 3.040 ... (remaining 252271 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.220 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.220 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 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 : 0.008 0.337 33960 Z= 0.484 Angle : 1.150 30.818 46059 Z= 0.712 Chirality : 0.060 0.337 5139 Planarity : 0.020 0.440 5736 Dihedral : 16.861 87.889 12252 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.02 % Favored : 89.79 % Rotamer: Outliers : 2.08 % Allowed : 24.38 % Favored : 73.54 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.13), residues: 4035 helix: 0.06 (0.10), residues: 2475 sheet: 0.82 (0.37), residues: 243 loop : -3.15 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1036 TYR 0.021 0.002 TYR C 995 PHE 0.034 0.002 PHE C1031 TRP 0.029 0.002 TRP A1996 HIS 0.005 0.001 HIS B1966 Details of bonding type rmsd covalent geometry : bond 0.00700 (33957) covalent geometry : angle 1.12386 (46053) SS BOND : bond 0.33650 ( 3) SS BOND : angle 21.24124 ( 6) hydrogen bonds : bond 0.17227 ( 1917) hydrogen bonds : angle 6.88670 ( 5697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 604 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 TYR cc_start: 0.1208 (OUTLIER) cc_final: 0.0479 (m-10) REVERT: A 887 MET cc_start: 0.2673 (mmm) cc_final: 0.2274 (mtp) REVERT: A 1210 MET cc_start: 0.2244 (ppp) cc_final: 0.0428 (tpt) REVERT: A 1275 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6949 (m-40) REVERT: A 1276 ASN cc_start: 0.7530 (t0) cc_final: 0.7283 (t0) REVERT: A 1302 PHE cc_start: 0.6689 (m-80) cc_final: 0.6487 (m-10) REVERT: A 1332 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3300 (tt0) REVERT: A 1379 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 1970 MET cc_start: 0.7581 (tpt) cc_final: 0.6867 (pmm) REVERT: A 2082 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: A 2231 ASP cc_start: 0.6389 (m-30) cc_final: 0.6079 (m-30) REVERT: A 2255 THR cc_start: 0.8800 (m) cc_final: 0.8502 (p) REVERT: A 2413 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: B 887 MET cc_start: 0.2480 (mmm) cc_final: 0.1896 (mtt) REVERT: B 1189 PHE cc_start: 0.7649 (m-10) cc_final: 0.7216 (m-80) REVERT: B 1210 MET cc_start: 0.2154 (ppp) cc_final: 0.0401 (tpt) REVERT: B 1289 LYS cc_start: 0.5942 (tmtt) cc_final: 0.5599 (mmmt) REVERT: B 1332 GLU cc_start: 0.3669 (OUTLIER) cc_final: 0.2775 (tt0) REVERT: B 1365 ILE cc_start: 0.7427 (mm) cc_final: 0.7214 (tp) REVERT: B 1379 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 1692 MET cc_start: 0.7431 (mtp) cc_final: 0.7121 (ptm) REVERT: B 1970 MET cc_start: 0.7567 (tpt) cc_final: 0.6737 (pmm) REVERT: B 2082 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7086 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6848 (m-30) cc_final: 0.6566 (m-30) REVERT: B 2284 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7430 (mtt180) REVERT: B 2413 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: C 878 TYR cc_start: 0.0868 (OUTLIER) cc_final: 0.0289 (m-10) REVERT: C 887 MET cc_start: 0.2525 (mmm) cc_final: 0.2211 (mtt) REVERT: C 1102 TRP cc_start: 0.7165 (m100) cc_final: 0.6734 (m100) REVERT: C 1189 PHE cc_start: 0.7704 (m-10) cc_final: 0.7238 (m-80) REVERT: C 1210 MET cc_start: 0.1721 (ppp) cc_final: 0.0015 (tpt) REVERT: C 1275 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.7129 (m-40) REVERT: C 1332 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.2814 (tt0) REVERT: C 1379 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 1692 MET cc_start: 0.7278 (mtp) cc_final: 0.7065 (ptm) REVERT: C 1970 MET cc_start: 0.7582 (tpt) cc_final: 0.6694 (pmm) REVERT: C 2058 PHE cc_start: 0.8485 (m-80) cc_final: 0.8281 (m-80) REVERT: C 2231 ASP cc_start: 0.6444 (m-30) cc_final: 0.6182 (m-30) REVERT: C 2413 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.6932 (tt0) outliers start: 75 outliers final: 21 residues processed: 656 average time/residue: 0.2345 time to fit residues: 242.3570 Evaluate side-chains 408 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 377 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 878 TYR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1275 ASN Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1976 PHE Chi-restraints excluded: chain A residue 2413 GLU Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1332 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 2413 GLU Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 841 PHE Chi-restraints excluded: chain C residue 878 TYR Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1034 ASN Chi-restraints excluded: chain C residue 1249 LEU Chi-restraints excluded: chain C residue 1275 ASN Chi-restraints excluded: chain C residue 1332 GLU Chi-restraints excluded: chain C residue 1372 ILE Chi-restraints excluded: chain C residue 1649 ASN Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 2413 GLU Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN A1675 GLN A2234 HIS B 987 ASN B1219 HIS ** B1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1675 GLN ** B2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2234 HIS ** C1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1675 GLN C1723 HIS C2234 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.188701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.149040 restraints weight = 61330.633| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.51 r_work: 0.3709 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33960 Z= 0.162 Angle : 0.742 13.077 46059 Z= 0.382 Chirality : 0.046 0.273 5139 Planarity : 0.006 0.111 5736 Dihedral : 6.738 68.676 4504 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.14 % Favored : 92.12 % Rotamer: Outliers : 4.21 % Allowed : 23.19 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.78 (0.13), residues: 4035 helix: 0.66 (0.10), residues: 2445 sheet: 0.82 (0.35), residues: 237 loop : -3.06 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1366 TYR 0.015 0.001 TYR B1208 PHE 0.021 0.002 PHE C1045 TRP 0.019 0.001 TRP C1996 HIS 0.012 0.001 HIS B1219 Details of bonding type rmsd covalent geometry : bond 0.00344 (33957) covalent geometry : angle 0.73991 (46053) SS BOND : bond 0.00665 ( 3) SS BOND : angle 4.53430 ( 6) hydrogen bonds : bond 0.05431 ( 1917) hydrogen bonds : angle 5.24454 ( 5697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 376 time to evaluate : 1.288 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 857 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7222 (tt) REVERT: A 887 MET cc_start: 0.2894 (mmm) cc_final: 0.2519 (mtt) REVERT: A 1017 MET cc_start: 0.7237 (mtt) cc_final: 0.6983 (tpp) REVERT: A 1086 ARG cc_start: 0.7851 (ptt-90) cc_final: 0.7455 (ptt-90) REVERT: A 1200 MET cc_start: 0.6757 (tpp) cc_final: 0.6445 (tpp) REVERT: A 1210 MET cc_start: 0.3166 (ppp) cc_final: 0.1281 (tpt) REVERT: A 1222 LYS cc_start: 0.4932 (OUTLIER) cc_final: 0.3822 (mtpt) REVERT: A 1267 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6961 (mm-40) REVERT: A 1276 ASN cc_start: 0.8261 (t0) cc_final: 0.7679 (t0) REVERT: A 1302 PHE cc_start: 0.7148 (m-80) cc_final: 0.6916 (m-10) REVERT: A 1379 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 1830 ASP cc_start: 0.6709 (t0) cc_final: 0.6422 (t0) REVERT: A 1922 MET cc_start: 0.7950 (mtt) cc_final: 0.7562 (mtm) REVERT: A 1970 MET cc_start: 0.7038 (tpt) cc_final: 0.6461 (ptm) REVERT: A 2082 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: A 2231 ASP cc_start: 0.6737 (m-30) cc_final: 0.6417 (m-30) REVERT: A 2255 THR cc_start: 0.8757 (m) cc_final: 0.8517 (p) REVERT: A 2413 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: B 887 MET cc_start: 0.2735 (mmm) cc_final: 0.2274 (mtt) REVERT: B 1200 MET cc_start: 0.7118 (tpp) cc_final: 0.6826 (tpp) REVERT: B 1210 MET cc_start: 0.2696 (ppp) cc_final: 0.0819 (tpt) REVERT: B 1222 LYS cc_start: 0.4780 (OUTLIER) cc_final: 0.3940 (mtpt) REVERT: B 1351 MET cc_start: 0.6531 (mmm) cc_final: 0.5717 (tpt) REVERT: B 1366 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6350 (ttp80) REVERT: B 1379 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 1681 TYR cc_start: 0.4727 (m-80) cc_final: 0.4502 (m-80) REVERT: B 1727 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6613 (mm) REVERT: B 1830 ASP cc_start: 0.7256 (t0) cc_final: 0.6937 (t0) REVERT: B 1922 MET cc_start: 0.7972 (mtt) cc_final: 0.7684 (mtm) REVERT: B 1936 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8866 (tp) REVERT: B 1970 MET cc_start: 0.7114 (tpt) cc_final: 0.6621 (ptm) REVERT: B 2049 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8427 (pt) REVERT: B 2082 ARG cc_start: 0.7526 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6965 (m-30) cc_final: 0.6506 (m-30) REVERT: B 2281 ASP cc_start: 0.8244 (t0) cc_final: 0.7907 (t0) REVERT: B 2436 MET cc_start: 0.7639 (mmt) cc_final: 0.6736 (mmt) REVERT: C 857 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7470 (tt) REVERT: C 1102 TRP cc_start: 0.7253 (m100) cc_final: 0.6730 (m100) REVERT: C 1200 MET cc_start: 0.6677 (tpp) cc_final: 0.6414 (tpp) REVERT: C 1210 MET cc_start: 0.2047 (ppp) cc_final: 0.0168 (tpt) REVERT: C 1222 LYS cc_start: 0.4830 (OUTLIER) cc_final: 0.3802 (mtpt) REVERT: C 1379 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 1727 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 1970 MET cc_start: 0.7142 (tpt) cc_final: 0.6476 (ptm) REVERT: C 1987 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: C 2049 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8443 (pt) REVERT: C 2218 MET cc_start: 0.7093 (tpt) cc_final: 0.6703 (mmp) REVERT: C 2371 LEU cc_start: 0.8139 (mp) cc_final: 0.7838 (tt) REVERT: C 2413 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7437 (tt0) outliers start: 152 outliers final: 61 residues processed: 495 average time/residue: 0.2022 time to fit residues: 165.0037 Evaluate side-chains 411 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 336 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1267 GLN Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2086 GLU Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2375 ILE Chi-restraints excluded: chain A residue 2413 GLU Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 878 TYR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1199 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1648 SER Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1873 THR Chi-restraints excluded: chain B residue 1936 LEU Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2375 ILE Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 841 PHE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1034 ASN Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1249 LEU Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1648 SER Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1730 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1873 THR Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2238 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2292 LEU Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2413 GLU Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 373 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 333 optimal weight: 0.2980 chunk 304 optimal weight: 0.9980 chunk 239 optimal weight: 0.0970 chunk 7 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 222 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 ASN B1219 HIS B1723 HIS ** B2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1219 HIS C1649 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.188913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.152445 restraints weight = 61653.117| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 2.70 r_work: 0.3727 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33960 Z= 0.134 Angle : 0.681 13.120 46059 Z= 0.347 Chirality : 0.044 0.246 5139 Planarity : 0.005 0.139 5736 Dihedral : 5.762 58.632 4468 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.31 % Favored : 91.92 % Rotamer: Outliers : 3.96 % Allowed : 23.00 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 4035 helix: 0.91 (0.10), residues: 2451 sheet: 0.92 (0.34), residues: 237 loop : -2.92 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1373 TYR 0.028 0.001 TYR A1681 PHE 0.026 0.001 PHE C1045 TRP 0.022 0.001 TRP C1733 HIS 0.016 0.001 HIS B1219 Details of bonding type rmsd covalent geometry : bond 0.00278 (33957) covalent geometry : angle 0.68002 (46053) SS BOND : bond 0.00020 ( 3) SS BOND : angle 2.56732 ( 6) hydrogen bonds : bond 0.04591 ( 1917) hydrogen bonds : angle 4.97755 ( 5697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 370 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 MET cc_start: 0.2916 (mmm) cc_final: 0.2408 (mtt) REVERT: A 1210 MET cc_start: 0.2943 (ppp) cc_final: 0.1134 (tpt) REVERT: A 1222 LYS cc_start: 0.4493 (OUTLIER) cc_final: 0.3584 (mtpt) REVERT: A 1276 ASN cc_start: 0.8078 (t0) cc_final: 0.7547 (t0) REVERT: A 1302 PHE cc_start: 0.7034 (m-80) cc_final: 0.6824 (m-10) REVERT: A 1351 MET cc_start: 0.6530 (mmt) cc_final: 0.6053 (mmm) REVERT: A 1370 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5974 (tp30) REVERT: A 1379 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 1877 MET cc_start: 0.7665 (mtp) cc_final: 0.7453 (mpp) REVERT: A 1922 MET cc_start: 0.7812 (mtt) cc_final: 0.7533 (mtm) REVERT: A 2001 MET cc_start: 0.7834 (mtt) cc_final: 0.7511 (mtp) REVERT: A 2082 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7178 (mtm-85) REVERT: A 2231 ASP cc_start: 0.6589 (m-30) cc_final: 0.6173 (m-30) REVERT: A 2255 THR cc_start: 0.8655 (m) cc_final: 0.8431 (p) REVERT: A 2304 MET cc_start: 0.8329 (ptm) cc_final: 0.7874 (ptp) REVERT: B 887 MET cc_start: 0.2636 (mmm) cc_final: 0.2129 (mtt) REVERT: B 1156 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.4509 (mmtt) REVERT: B 1210 MET cc_start: 0.2771 (ppp) cc_final: 0.1077 (tpt) REVERT: B 1222 LYS cc_start: 0.4668 (OUTLIER) cc_final: 0.3944 (mtpt) REVERT: B 1235 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5366 (tt) REVERT: B 1379 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 1715 VAL cc_start: 0.5543 (OUTLIER) cc_final: 0.5333 (m) REVERT: B 1727 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6465 (mm) REVERT: B 1877 MET cc_start: 0.7783 (mtp) cc_final: 0.7541 (mpp) REVERT: B 1881 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6265 (mtp) REVERT: B 1922 MET cc_start: 0.7912 (mtt) cc_final: 0.7640 (mtm) REVERT: B 2045 MET cc_start: 0.7342 (mtt) cc_final: 0.7113 (ttt) REVERT: B 2049 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8333 (pt) REVERT: B 2082 ARG cc_start: 0.7238 (mtm-85) cc_final: 0.6846 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6628 (m-30) cc_final: 0.6180 (m-30) REVERT: C 1102 TRP cc_start: 0.7404 (m100) cc_final: 0.6940 (m100) REVERT: C 1200 MET cc_start: 0.6909 (tpp) cc_final: 0.6537 (tpp) REVERT: C 1210 MET cc_start: 0.1871 (ppp) cc_final: 0.0095 (tpt) REVERT: C 1222 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.3841 (mtpt) REVERT: C 1351 MET cc_start: 0.6500 (mmt) cc_final: 0.6057 (mmp) REVERT: C 1379 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 1405 MET cc_start: 0.7304 (ptp) cc_final: 0.6897 (ptp) REVERT: C 1715 VAL cc_start: 0.5540 (OUTLIER) cc_final: 0.5332 (m) REVERT: C 1970 MET cc_start: 0.6658 (tpt) cc_final: 0.6375 (ptm) REVERT: C 1987 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: C 2049 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8449 (pt) REVERT: C 2218 MET cc_start: 0.6840 (tpt) cc_final: 0.6450 (mmp) outliers start: 143 outliers final: 55 residues processed: 482 average time/residue: 0.2146 time to fit residues: 169.6025 Evaluate side-chains 400 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 332 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1883 LEU Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2086 GLU Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 878 TYR Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1873 THR Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 841 PHE Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1715 VAL Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1873 THR Chi-restraints excluded: chain C residue 1874 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2238 ILE Chi-restraints excluded: chain C residue 2272 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 108 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 400 optimal weight: 0.0970 chunk 352 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 121 optimal weight: 0.0050 chunk 145 optimal weight: 6.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1818 HIS A2206 HIS B 987 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.187568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.153363 restraints weight = 61523.957| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.71 r_work: 0.3702 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33960 Z= 0.144 Angle : 0.669 13.749 46059 Z= 0.345 Chirality : 0.045 0.335 5139 Planarity : 0.005 0.113 5736 Dihedral : 5.552 59.098 4456 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.79 % Favored : 92.32 % Rotamer: Outliers : 4.13 % Allowed : 22.25 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.31 (0.13), residues: 4035 helix: 0.94 (0.10), residues: 2484 sheet: 0.91 (0.34), residues: 237 loop : -2.74 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1373 TYR 0.017 0.001 TYR A1208 PHE 0.035 0.001 PHE B 825 TRP 0.013 0.001 TRP A1996 HIS 0.009 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00319 (33957) covalent geometry : angle 0.66918 (46053) SS BOND : bond 0.00188 ( 3) SS BOND : angle 1.83836 ( 6) hydrogen bonds : bond 0.04550 ( 1917) hydrogen bonds : angle 4.87666 ( 5697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 351 time to evaluate : 1.278 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 875 MET cc_start: 0.4007 (ptt) cc_final: 0.3503 (mmt) REVERT: A 887 MET cc_start: 0.3169 (mmm) cc_final: 0.2670 (mtt) REVERT: A 1210 MET cc_start: 0.3105 (ppp) cc_final: 0.1300 (tpt) REVERT: A 1276 ASN cc_start: 0.8025 (t0) cc_final: 0.7550 (t0) REVERT: A 1302 PHE cc_start: 0.7077 (m-80) cc_final: 0.6794 (m-10) REVERT: A 1351 MET cc_start: 0.6622 (mmt) cc_final: 0.6111 (mmm) REVERT: A 1370 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6138 (tp30) REVERT: A 1379 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 1727 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (mm) REVERT: A 1877 MET cc_start: 0.7690 (mtp) cc_final: 0.7464 (mpp) REVERT: A 1922 MET cc_start: 0.7931 (mtt) cc_final: 0.7350 (mtm) REVERT: A 2026 GLU cc_start: 0.6682 (pp20) cc_final: 0.6426 (pt0) REVERT: A 2082 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7151 (mtm-85) REVERT: A 2231 ASP cc_start: 0.6708 (m-30) cc_final: 0.6329 (m-30) REVERT: A 2255 THR cc_start: 0.8655 (m) cc_final: 0.8436 (p) REVERT: B 875 MET cc_start: 0.5085 (ptm) cc_final: 0.4132 (mtt) REVERT: B 887 MET cc_start: 0.2641 (mmm) cc_final: 0.2239 (mtt) REVERT: B 1156 LYS cc_start: 0.4673 (OUTLIER) cc_final: 0.4406 (mmtt) REVERT: B 1210 MET cc_start: 0.2653 (ppp) cc_final: 0.1049 (tpt) REVERT: B 1222 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.3904 (mtpt) REVERT: B 1235 ILE cc_start: 0.5560 (OUTLIER) cc_final: 0.5245 (tt) REVERT: B 1351 MET cc_start: 0.6345 (mmt) cc_final: 0.5720 (mmm) REVERT: B 1379 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 1392 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6783 (p) REVERT: B 1727 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6466 (mm) REVERT: B 1877 MET cc_start: 0.7878 (mtp) cc_final: 0.7649 (mpp) REVERT: B 1922 MET cc_start: 0.7918 (mtt) cc_final: 0.7685 (mtm) REVERT: B 1925 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7477 (mtp85) REVERT: B 2045 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6993 (ttt) REVERT: B 2082 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.6971 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6779 (m-30) cc_final: 0.6399 (m-30) REVERT: B 2281 ASP cc_start: 0.8106 (t0) cc_final: 0.7840 (t0) REVERT: C 875 MET cc_start: 0.4436 (ptt) cc_final: 0.3455 (mmt) REVERT: C 1028 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6552 (mt) REVERT: C 1086 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7711 (ptm-80) REVERT: C 1102 TRP cc_start: 0.7431 (m100) cc_final: 0.7062 (m100) REVERT: C 1210 MET cc_start: 0.1932 (ppp) cc_final: 0.0227 (tpt) REVERT: C 1222 LYS cc_start: 0.4783 (OUTLIER) cc_final: 0.3942 (mtpt) REVERT: C 1351 MET cc_start: 0.6296 (mmt) cc_final: 0.5892 (mmp) REVERT: C 1379 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8216 (tm-30) REVERT: C 1392 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.6978 (p) REVERT: C 1405 MET cc_start: 0.7326 (ptp) cc_final: 0.6935 (ptp) REVERT: C 1726 MET cc_start: 0.6489 (tmm) cc_final: 0.6134 (mtt) REVERT: C 1727 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6622 (mm) REVERT: C 1945 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8028 (mt) REVERT: C 1970 MET cc_start: 0.6702 (tpt) cc_final: 0.6473 (ptm) REVERT: C 1987 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: C 2026 GLU cc_start: 0.6667 (pp20) cc_final: 0.6317 (pt0) REVERT: C 2049 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (pt) REVERT: C 2094 MET cc_start: 0.8757 (tpp) cc_final: 0.7638 (tpp) REVERT: C 2218 MET cc_start: 0.6912 (tpt) cc_final: 0.6532 (mmp) outliers start: 149 outliers final: 74 residues processed: 474 average time/residue: 0.2067 time to fit residues: 162.4731 Evaluate side-chains 428 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 339 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 995 TYR Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1883 LEU Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2086 GLU Chi-restraints excluded: chain A residue 2102 ASP Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 995 TYR Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1156 LYS Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1873 THR Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2102 ASP Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 841 PHE Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 995 TYR Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1235 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1392 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1945 LEU Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2242 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 0.0470 chunk 303 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 332 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 402 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1136 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B1136 ASN C2206 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.187672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.152942 restraints weight = 61605.427| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.73 r_work: 0.3699 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33960 Z= 0.135 Angle : 0.640 13.544 46059 Z= 0.330 Chirality : 0.043 0.265 5139 Planarity : 0.005 0.101 5736 Dihedral : 5.415 56.145 4456 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.79 % Favored : 92.32 % Rotamer: Outliers : 4.24 % Allowed : 22.25 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.13), residues: 4035 helix: 1.10 (0.10), residues: 2478 sheet: 0.77 (0.34), residues: 237 loop : -2.72 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1366 TYR 0.024 0.001 TYR B1681 PHE 0.031 0.001 PHE B 825 TRP 0.024 0.001 TRP A1077 HIS 0.007 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00301 (33957) covalent geometry : angle 0.63993 (46053) SS BOND : bond 0.00125 ( 3) SS BOND : angle 1.71516 ( 6) hydrogen bonds : bond 0.04303 ( 1917) hydrogen bonds : angle 4.75398 ( 5697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 352 time to evaluate : 1.437 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 875 MET cc_start: 0.4027 (ptt) cc_final: 0.3726 (tpt) REVERT: A 887 MET cc_start: 0.3273 (mmm) cc_final: 0.2589 (mtt) REVERT: A 1200 MET cc_start: 0.6908 (tpp) cc_final: 0.6554 (tpp) REVERT: A 1210 MET cc_start: 0.2995 (ppp) cc_final: 0.1258 (tpt) REVERT: A 1222 LYS cc_start: 0.4156 (OUTLIER) cc_final: 0.3476 (mtpt) REVERT: A 1276 ASN cc_start: 0.7997 (t0) cc_final: 0.7576 (t0) REVERT: A 1351 MET cc_start: 0.6444 (mmt) cc_final: 0.5991 (mmm) REVERT: A 1379 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 1701 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 1877 MET cc_start: 0.7654 (mtp) cc_final: 0.7452 (mpp) REVERT: A 2026 GLU cc_start: 0.6763 (pp20) cc_final: 0.6526 (pt0) REVERT: A 2082 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: A 2113 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: A 2231 ASP cc_start: 0.6689 (m-30) cc_final: 0.6365 (m-30) REVERT: A 2255 THR cc_start: 0.8620 (m) cc_final: 0.8411 (p) REVERT: B 875 MET cc_start: 0.5035 (ptm) cc_final: 0.4781 (tpt) REVERT: B 887 MET cc_start: 0.2567 (mmm) cc_final: 0.2162 (mtt) REVERT: B 983 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5453 (tmm160) REVERT: B 1006 MET cc_start: 0.5955 (tpp) cc_final: 0.5539 (tpp) REVERT: B 1086 ARG cc_start: 0.7972 (ptt-90) cc_final: 0.7649 (ptt-90) REVERT: B 1188 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5756 (tt) REVERT: B 1200 MET cc_start: 0.6571 (tpp) cc_final: 0.6262 (tpp) REVERT: B 1210 MET cc_start: 0.2307 (ppp) cc_final: 0.0759 (tpt) REVERT: B 1222 LYS cc_start: 0.4558 (OUTLIER) cc_final: 0.3916 (mtpt) REVERT: B 1235 ILE cc_start: 0.5495 (OUTLIER) cc_final: 0.5192 (tt) REVERT: B 1237 MET cc_start: 0.7426 (tpp) cc_final: 0.7191 (tpp) REVERT: B 1351 MET cc_start: 0.6400 (mmt) cc_final: 0.5802 (mmm) REVERT: B 1372 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6516 (tt) REVERT: B 1379 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 1392 VAL cc_start: 0.7119 (OUTLIER) cc_final: 0.6838 (p) REVERT: B 1405 MET cc_start: 0.7251 (ptp) cc_final: 0.7021 (ptp) REVERT: B 1726 MET cc_start: 0.6754 (tmm) cc_final: 0.6446 (mtt) REVERT: B 1727 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6486 (mm) REVERT: B 1877 MET cc_start: 0.7856 (mtp) cc_final: 0.7631 (mpp) REVERT: B 1922 MET cc_start: 0.7799 (mtt) cc_final: 0.7313 (mtm) REVERT: B 1925 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7367 (mtp85) REVERT: B 2045 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7105 (mtp) REVERT: B 2082 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6966 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6868 (m-30) cc_final: 0.6474 (m-30) REVERT: B 2281 ASP cc_start: 0.8007 (t0) cc_final: 0.7804 (t0) REVERT: C 875 MET cc_start: 0.4365 (ptt) cc_final: 0.3631 (tpt) REVERT: C 1028 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6694 (mt) REVERT: C 1102 TRP cc_start: 0.7454 (m100) cc_final: 0.7179 (m100) REVERT: C 1210 MET cc_start: 0.1732 (ppp) cc_final: 0.0161 (tpt) REVERT: C 1379 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8249 (tm-30) REVERT: C 1392 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 1405 MET cc_start: 0.7347 (ptp) cc_final: 0.6958 (ptp) REVERT: C 1726 MET cc_start: 0.6450 (tmm) cc_final: 0.6163 (mtt) REVERT: C 1727 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6807 (mm) REVERT: C 1922 MET cc_start: 0.7523 (mtm) cc_final: 0.7160 (mtp) REVERT: C 1987 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: C 2049 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8471 (pt) REVERT: C 2218 MET cc_start: 0.6897 (tpt) cc_final: 0.6503 (mmp) outliers start: 153 outliers final: 83 residues processed: 474 average time/residue: 0.1971 time to fit residues: 155.5293 Evaluate side-chains 442 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 343 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1402 ASP Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 PHE Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1883 LEU Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2102 ASP Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1064 LEU Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1188 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1697 LEU Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1730 LEU Chi-restraints excluded: chain B residue 1873 THR Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1883 LEU Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2102 ASP Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 THR Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1392 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1874 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2112 ASP Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 193 optimal weight: 8.9990 chunk 388 optimal weight: 0.2980 chunk 355 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B 977 HIS B1131 ASN B1818 HIS C1034 ASN C1131 ASN C2206 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.187685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152582 restraints weight = 61892.264| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.72 r_work: 0.3704 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33960 Z= 0.132 Angle : 0.635 13.367 46059 Z= 0.327 Chirality : 0.043 0.264 5139 Planarity : 0.005 0.094 5736 Dihedral : 5.009 42.803 4444 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.86 % Favored : 92.24 % Rotamer: Outliers : 3.85 % Allowed : 22.72 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.11 (0.13), residues: 4035 helix: 1.13 (0.10), residues: 2487 sheet: 0.69 (0.33), residues: 237 loop : -2.68 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1366 TYR 0.020 0.001 TYR C1892 PHE 0.030 0.001 PHE B1045 TRP 0.019 0.001 TRP B1077 HIS 0.005 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00295 (33957) covalent geometry : angle 0.63511 (46053) SS BOND : bond 0.00119 ( 3) SS BOND : angle 1.61118 ( 6) hydrogen bonds : bond 0.04217 ( 1917) hydrogen bonds : angle 4.71739 ( 5697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 349 time to evaluate : 1.231 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 875 MET cc_start: 0.4173 (ptt) cc_final: 0.3801 (tpt) REVERT: A 887 MET cc_start: 0.3382 (mmm) cc_final: 0.2592 (mtt) REVERT: A 1200 MET cc_start: 0.6995 (tpp) cc_final: 0.6717 (tpp) REVERT: A 1210 MET cc_start: 0.2988 (ppp) cc_final: 0.1284 (tpt) REVERT: A 1222 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3468 (mtpt) REVERT: A 1260 LYS cc_start: 0.7633 (tttt) cc_final: 0.6957 (tptp) REVERT: A 1276 ASN cc_start: 0.7998 (t0) cc_final: 0.7600 (t0) REVERT: A 1351 MET cc_start: 0.6424 (mmt) cc_final: 0.5987 (mmm) REVERT: A 1379 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 1628 MET cc_start: 0.8205 (mmt) cc_final: 0.7961 (mmm) REVERT: A 1701 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 2082 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7210 (mtm-85) REVERT: A 2113 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: A 2231 ASP cc_start: 0.6685 (m-30) cc_final: 0.6369 (m-30) REVERT: A 2255 THR cc_start: 0.8614 (m) cc_final: 0.8402 (p) REVERT: A 2371 LEU cc_start: 0.8190 (mp) cc_final: 0.7837 (tt) REVERT: B 887 MET cc_start: 0.2473 (mmm) cc_final: 0.2040 (mtt) REVERT: B 983 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5300 (tmm160) REVERT: B 1006 MET cc_start: 0.5657 (tpp) cc_final: 0.5282 (tpp) REVERT: B 1188 LEU cc_start: 0.6106 (tt) cc_final: 0.5798 (tt) REVERT: B 1200 MET cc_start: 0.6715 (tpp) cc_final: 0.6433 (tpp) REVERT: B 1210 MET cc_start: 0.2432 (ppp) cc_final: 0.0844 (tpt) REVERT: B 1222 LYS cc_start: 0.4509 (OUTLIER) cc_final: 0.3899 (mtpt) REVERT: B 1235 ILE cc_start: 0.5513 (OUTLIER) cc_final: 0.5211 (tt) REVERT: B 1351 MET cc_start: 0.6393 (mmt) cc_final: 0.5815 (mmm) REVERT: B 1379 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 1392 VAL cc_start: 0.7115 (OUTLIER) cc_final: 0.6824 (p) REVERT: B 1405 MET cc_start: 0.7213 (ptp) cc_final: 0.6973 (ptp) REVERT: B 1726 MET cc_start: 0.6651 (tmm) cc_final: 0.6331 (mtt) REVERT: B 1727 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6482 (mm) REVERT: B 2045 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7068 (mtp) REVERT: B 2082 ARG cc_start: 0.7381 (mtm-85) cc_final: 0.6976 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6792 (m-30) cc_final: 0.6403 (m-30) REVERT: C 858 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7028 (p) REVERT: C 875 MET cc_start: 0.4245 (ptt) cc_final: 0.3580 (tpt) REVERT: C 1028 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6712 (mt) REVERT: C 1102 TRP cc_start: 0.7472 (m100) cc_final: 0.7224 (m100) REVERT: C 1210 MET cc_start: 0.2038 (ppp) cc_final: 0.0436 (tpt) REVERT: C 1222 LYS cc_start: 0.4602 (OUTLIER) cc_final: 0.3837 (mtpt) REVERT: C 1379 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8193 (tm-30) REVERT: C 1392 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6991 (p) REVERT: C 1405 MET cc_start: 0.7313 (ptp) cc_final: 0.6918 (ptp) REVERT: C 1726 MET cc_start: 0.6477 (tmm) cc_final: 0.6209 (mtt) REVERT: C 1727 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6797 (mm) REVERT: C 1987 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: C 2049 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (pt) REVERT: C 2094 MET cc_start: 0.8735 (tpp) cc_final: 0.7615 (tpp) REVERT: C 2218 MET cc_start: 0.6925 (tpt) cc_final: 0.6520 (mmp) outliers start: 139 outliers final: 93 residues processed: 459 average time/residue: 0.1999 time to fit residues: 151.6846 Evaluate side-chains 446 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 337 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 991 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1165 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 PHE Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1883 LEU Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2102 ASP Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 991 PHE Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain B residue 1165 PHE Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1873 THR Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2102 ASP Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2403 LEU Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 991 PHE Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1034 ASN Chi-restraints excluded: chain C residue 1165 PHE Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1295 THR Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1392 VAL Chi-restraints excluded: chain C residue 1667 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1874 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2099 SER Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 212 optimal weight: 0.0670 chunk 291 optimal weight: 8.9990 chunk 125 optimal weight: 0.4980 chunk 325 optimal weight: 0.0570 chunk 250 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B1094 ASN B1131 ASN C1034 ASN C1131 ASN C1318 HIS C2206 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.188473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.153910 restraints weight = 61773.087| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.74 r_work: 0.3716 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33960 Z= 0.123 Angle : 0.626 13.272 46059 Z= 0.322 Chirality : 0.043 0.255 5139 Planarity : 0.005 0.088 5736 Dihedral : 4.931 42.484 4444 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.79 % Favored : 92.32 % Rotamer: Outliers : 3.85 % Allowed : 23.11 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.06 (0.13), residues: 4035 helix: 1.17 (0.10), residues: 2487 sheet: 0.70 (0.33), residues: 237 loop : -2.65 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1366 TYR 0.021 0.001 TYR C1892 PHE 0.046 0.001 PHE C 825 TRP 0.020 0.001 TRP B1077 HIS 0.004 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00265 (33957) covalent geometry : angle 0.62539 (46053) SS BOND : bond 0.00102 ( 3) SS BOND : angle 1.53085 ( 6) hydrogen bonds : bond 0.03980 ( 1917) hydrogen bonds : angle 4.67037 ( 5697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 347 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 MET cc_start: 0.3313 (mmm) cc_final: 0.2521 (mtt) REVERT: A 957 HIS cc_start: -0.0560 (OUTLIER) cc_final: -0.0778 (m170) REVERT: A 1200 MET cc_start: 0.7204 (tpp) cc_final: 0.6953 (tpp) REVERT: A 1210 MET cc_start: 0.2910 (ppp) cc_final: 0.1369 (tpt) REVERT: A 1222 LYS cc_start: 0.4244 (OUTLIER) cc_final: 0.3502 (mtpt) REVERT: A 1260 LYS cc_start: 0.7552 (tttt) cc_final: 0.6894 (tptp) REVERT: A 1276 ASN cc_start: 0.7957 (t0) cc_final: 0.7595 (t0) REVERT: A 1351 MET cc_start: 0.6491 (mmt) cc_final: 0.6040 (mmm) REVERT: A 1379 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 1628 MET cc_start: 0.8209 (mmt) cc_final: 0.7960 (mmm) REVERT: A 1701 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7970 (t80) REVERT: A 2082 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.7018 (mtm-85) REVERT: A 2113 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: A 2231 ASP cc_start: 0.6667 (m-30) cc_final: 0.6218 (m-30) REVERT: A 2255 THR cc_start: 0.8609 (m) cc_final: 0.8387 (p) REVERT: A 2347 PHE cc_start: 0.7200 (p90) cc_final: 0.6882 (p90) REVERT: B 887 MET cc_start: 0.2447 (mmm) cc_final: 0.2028 (mtt) REVERT: B 957 HIS cc_start: -0.0452 (OUTLIER) cc_final: -0.0851 (m170) REVERT: B 983 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5068 (ptt-90) REVERT: B 1086 ARG cc_start: 0.7805 (ptt-90) cc_final: 0.7541 (ptt-90) REVERT: B 1131 ASN cc_start: 0.4307 (OUTLIER) cc_final: 0.3762 (m110) REVERT: B 1188 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5847 (tt) REVERT: B 1200 MET cc_start: 0.6887 (tpp) cc_final: 0.6641 (tpp) REVERT: B 1210 MET cc_start: 0.2309 (ppp) cc_final: 0.0790 (tpt) REVERT: B 1222 LYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3818 (mtpt) REVERT: B 1235 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5225 (tt) REVERT: B 1351 MET cc_start: 0.6366 (mmt) cc_final: 0.5787 (mmm) REVERT: B 1379 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 1392 VAL cc_start: 0.7118 (OUTLIER) cc_final: 0.6824 (p) REVERT: B 1405 MET cc_start: 0.7204 (ptp) cc_final: 0.6930 (ptp) REVERT: B 1701 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 1727 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6480 (mm) REVERT: B 2045 MET cc_start: 0.7231 (mtt) cc_final: 0.6991 (mtp) REVERT: B 2082 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.6910 (mtm-85) REVERT: B 2094 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7971 (mmm) REVERT: B 2231 ASP cc_start: 0.6692 (m-30) cc_final: 0.6273 (m-30) REVERT: B 2284 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7705 (mtt180) REVERT: B 2347 PHE cc_start: 0.7406 (p90) cc_final: 0.7117 (p90) REVERT: C 858 SER cc_start: 0.7400 (OUTLIER) cc_final: 0.6976 (p) REVERT: C 875 MET cc_start: 0.3992 (ptt) cc_final: 0.3464 (tpt) REVERT: C 1028 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6768 (mt) REVERT: C 1102 TRP cc_start: 0.7479 (m100) cc_final: 0.7274 (m100) REVERT: C 1205 ASN cc_start: 0.4051 (t0) cc_final: 0.3679 (m110) REVERT: C 1210 MET cc_start: 0.2058 (ppp) cc_final: 0.0482 (tpt) REVERT: C 1222 LYS cc_start: 0.4379 (OUTLIER) cc_final: 0.3732 (mtpt) REVERT: C 1379 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8189 (tm-30) REVERT: C 1392 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.7002 (p) REVERT: C 1405 MET cc_start: 0.7342 (ptp) cc_final: 0.6922 (ptp) REVERT: C 1726 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.6275 (mtt) REVERT: C 1727 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6747 (mm) REVERT: C 1987 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: C 2049 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (pt) REVERT: C 2094 MET cc_start: 0.8696 (tpp) cc_final: 0.7608 (tpp) REVERT: C 2218 MET cc_start: 0.6940 (tpt) cc_final: 0.6545 (mmp) outliers start: 139 outliers final: 88 residues processed: 458 average time/residue: 0.2083 time to fit residues: 157.2741 Evaluate side-chains 443 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 333 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 957 HIS Chi-restraints excluded: chain A residue 991 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1165 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1201 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1402 ASP Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 PHE Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 957 HIS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 991 PHE Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain B residue 1165 PHE Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1188 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1315 ARG Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1883 LEU Chi-restraints excluded: chain B residue 1970 MET Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2094 MET Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2403 LEU Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 991 PHE Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1131 ASN Chi-restraints excluded: chain C residue 1165 PHE Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 THR Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1235 ILE Chi-restraints excluded: chain C residue 1295 THR Chi-restraints excluded: chain C residue 1315 ARG Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1392 VAL Chi-restraints excluded: chain C residue 1667 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1726 MET Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2099 SER Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 244 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 337 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 340 optimal weight: 3.9990 chunk 369 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN A1131 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B1131 ASN C1131 ASN C1904 GLN C2206 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.188026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.152919 restraints weight = 61287.810| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.78 r_work: 0.3700 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33960 Z= 0.145 Angle : 0.646 14.773 46059 Z= 0.333 Chirality : 0.044 0.329 5139 Planarity : 0.005 0.084 5736 Dihedral : 4.975 42.591 4444 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.97 % Allowed : 6.82 % Favored : 92.22 % Rotamer: Outliers : 3.66 % Allowed : 23.22 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.09 (0.13), residues: 4035 helix: 1.14 (0.10), residues: 2478 sheet: 0.57 (0.33), residues: 237 loop : -2.62 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1086 TYR 0.019 0.001 TYR C1892 PHE 0.050 0.002 PHE B 825 TRP 0.020 0.001 TRP A1077 HIS 0.004 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00333 (33957) covalent geometry : angle 0.64609 (46053) SS BOND : bond 0.00169 ( 3) SS BOND : angle 1.56548 ( 6) hydrogen bonds : bond 0.04301 ( 1917) hydrogen bonds : angle 4.70714 ( 5697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 338 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 MET cc_start: 0.3077 (mmm) cc_final: 0.2351 (mtt) REVERT: A 1200 MET cc_start: 0.7109 (tpp) cc_final: 0.6895 (tpp) REVERT: A 1210 MET cc_start: 0.3030 (ppp) cc_final: 0.1449 (tpt) REVERT: A 1222 LYS cc_start: 0.4299 (OUTLIER) cc_final: 0.3503 (mtpt) REVERT: A 1260 LYS cc_start: 0.7595 (tttt) cc_final: 0.6904 (tptp) REVERT: A 1276 ASN cc_start: 0.7957 (t0) cc_final: 0.7613 (t0) REVERT: A 1628 MET cc_start: 0.8212 (mmt) cc_final: 0.7950 (mmm) REVERT: A 1701 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 2026 GLU cc_start: 0.6927 (pp20) cc_final: 0.6659 (pt0) REVERT: A 2113 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: A 2231 ASP cc_start: 0.6770 (m-30) cc_final: 0.6427 (m-30) REVERT: A 2255 THR cc_start: 0.8610 (m) cc_final: 0.8393 (p) REVERT: A 2347 PHE cc_start: 0.7238 (p90) cc_final: 0.6913 (p90) REVERT: B 875 MET cc_start: 0.2681 (OUTLIER) cc_final: 0.2407 (ptt) REVERT: B 887 MET cc_start: 0.2437 (mmm) cc_final: 0.2083 (mtt) REVERT: B 957 HIS cc_start: -0.0211 (OUTLIER) cc_final: -0.0620 (m90) REVERT: B 983 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5350 (tmm160) REVERT: B 1006 MET cc_start: 0.5640 (tpp) cc_final: 0.5400 (tpp) REVERT: B 1086 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7633 (ptt-90) REVERT: B 1188 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5998 (tt) REVERT: B 1200 MET cc_start: 0.6763 (tpp) cc_final: 0.6555 (tpp) REVERT: B 1210 MET cc_start: 0.2517 (ppp) cc_final: 0.1147 (tpt) REVERT: B 1222 LYS cc_start: 0.4334 (OUTLIER) cc_final: 0.3786 (mtpt) REVERT: B 1235 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.5263 (tt) REVERT: B 1351 MET cc_start: 0.6242 (mmt) cc_final: 0.5729 (mmm) REVERT: B 1379 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8020 (tp40) REVERT: B 1392 VAL cc_start: 0.7120 (OUTLIER) cc_final: 0.6834 (p) REVERT: B 1405 MET cc_start: 0.7246 (ptp) cc_final: 0.6996 (ptp) REVERT: B 1701 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8148 (t80) REVERT: B 1727 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6574 (mm) REVERT: B 2082 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7047 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6770 (m-30) cc_final: 0.6373 (m-30) REVERT: B 2347 PHE cc_start: 0.7467 (p90) cc_final: 0.7173 (p90) REVERT: C 858 SER cc_start: 0.7442 (OUTLIER) cc_final: 0.7029 (p) REVERT: C 875 MET cc_start: 0.3937 (ptt) cc_final: 0.3437 (tpt) REVERT: C 957 HIS cc_start: -0.0074 (OUTLIER) cc_final: -0.0470 (m170) REVERT: C 1210 MET cc_start: 0.2103 (ppp) cc_final: 0.0667 (tpt) REVERT: C 1222 LYS cc_start: 0.4413 (OUTLIER) cc_final: 0.3800 (mtpt) REVERT: C 1351 MET cc_start: 0.6181 (mmt) cc_final: 0.5729 (mmm) REVERT: C 1379 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 1392 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.7027 (p) REVERT: C 1405 MET cc_start: 0.7314 (ptp) cc_final: 0.6890 (ptp) REVERT: C 1726 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6280 (mtt) REVERT: C 1727 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6829 (mm) REVERT: C 1987 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: C 2049 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8473 (pt) REVERT: C 2094 MET cc_start: 0.8772 (tpp) cc_final: 0.7785 (tpp) REVERT: C 2218 MET cc_start: 0.7035 (tpt) cc_final: 0.6627 (mmp) REVERT: C 2347 PHE cc_start: 0.7147 (p90) cc_final: 0.6824 (p90) outliers start: 132 outliers final: 96 residues processed: 446 average time/residue: 0.2043 time to fit residues: 149.7854 Evaluate side-chains 441 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 325 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1165 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1242 GLN Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1402 ASP Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 PHE Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1874 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2102 ASP Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2184 VAL Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2404 VAL Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 957 HIS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain B residue 1165 PHE Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1188 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1372 ILE Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1402 ASP Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1883 LEU Chi-restraints excluded: chain B residue 1970 MET Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 957 HIS Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1131 ASN Chi-restraints excluded: chain C residue 1165 PHE Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 THR Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1235 ILE Chi-restraints excluded: chain C residue 1295 THR Chi-restraints excluded: chain C residue 1315 ARG Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1392 VAL Chi-restraints excluded: chain C residue 1667 VAL Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1715 VAL Chi-restraints excluded: chain C residue 1726 MET Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1960 ILE Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2099 SER Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2242 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 293 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 350 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 325 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1131 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B1267 GLN B1318 HIS C1131 ASN C2206 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.187840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.152571 restraints weight = 61016.645| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.78 r_work: 0.3701 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33960 Z= 0.144 Angle : 0.651 15.301 46059 Z= 0.336 Chirality : 0.044 0.335 5139 Planarity : 0.005 0.080 5736 Dihedral : 4.997 43.124 4444 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.91 % Favored : 92.17 % Rotamer: Outliers : 3.57 % Allowed : 23.25 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.08 (0.13), residues: 4035 helix: 1.14 (0.10), residues: 2484 sheet: 0.55 (0.33), residues: 237 loop : -2.61 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1368 TYR 0.055 0.001 TYR A 953 PHE 0.053 0.002 PHE B 825 TRP 0.020 0.001 TRP B1077 HIS 0.013 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00327 (33957) covalent geometry : angle 0.65125 (46053) SS BOND : bond 0.00162 ( 3) SS BOND : angle 1.67572 ( 6) hydrogen bonds : bond 0.04289 ( 1917) hydrogen bonds : angle 4.69703 ( 5697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 329 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 MET cc_start: 0.3081 (mmm) cc_final: 0.2358 (mtt) REVERT: A 1200 MET cc_start: 0.7105 (tpp) cc_final: 0.6903 (tpp) REVERT: A 1210 MET cc_start: 0.3017 (ppp) cc_final: 0.1472 (tpt) REVERT: A 1222 LYS cc_start: 0.4324 (OUTLIER) cc_final: 0.3534 (mtpt) REVERT: A 1260 LYS cc_start: 0.7568 (tttt) cc_final: 0.6814 (tptp) REVERT: A 1276 ASN cc_start: 0.7954 (t0) cc_final: 0.7621 (t0) REVERT: A 1628 MET cc_start: 0.8215 (mmt) cc_final: 0.7955 (mmm) REVERT: A 1701 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7948 (t80) REVERT: A 2026 GLU cc_start: 0.6960 (pp20) cc_final: 0.6685 (pt0) REVERT: A 2113 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: A 2231 ASP cc_start: 0.6809 (m-30) cc_final: 0.6467 (m-30) REVERT: A 2347 PHE cc_start: 0.7356 (p90) cc_final: 0.7024 (p90) REVERT: B 887 MET cc_start: 0.2383 (mmm) cc_final: 0.2022 (mtt) REVERT: B 957 HIS cc_start: -0.0264 (OUTLIER) cc_final: -0.0617 (m90) REVERT: B 983 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5349 (tmm160) REVERT: B 1006 MET cc_start: 0.5684 (tpp) cc_final: 0.5473 (tpp) REVERT: B 1086 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.7507 (ptt-90) REVERT: B 1188 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6071 (tt) REVERT: B 1200 MET cc_start: 0.6787 (tpp) cc_final: 0.6454 (tpp) REVERT: B 1210 MET cc_start: 0.2546 (ppp) cc_final: 0.1124 (tpt) REVERT: B 1222 LYS cc_start: 0.4311 (OUTLIER) cc_final: 0.3808 (mtpt) REVERT: B 1235 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5283 (tt) REVERT: B 1294 GLU cc_start: 0.7346 (tp30) cc_final: 0.6866 (tt0) REVERT: B 1392 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6884 (p) REVERT: B 1405 MET cc_start: 0.7318 (ptp) cc_final: 0.7047 (ptp) REVERT: B 1701 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 1727 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6550 (mm) REVERT: B 2082 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7083 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6841 (m-30) cc_final: 0.6443 (m-30) REVERT: B 2347 PHE cc_start: 0.7477 (p90) cc_final: 0.7179 (p90) REVERT: C 858 SER cc_start: 0.7427 (OUTLIER) cc_final: 0.7041 (p) REVERT: C 875 MET cc_start: 0.3646 (ptt) cc_final: 0.3303 (tpt) REVERT: C 957 HIS cc_start: 0.0017 (OUTLIER) cc_final: -0.0187 (m170) REVERT: C 1210 MET cc_start: 0.2167 (ppp) cc_final: 0.0770 (tpt) REVERT: C 1222 LYS cc_start: 0.4381 (OUTLIER) cc_final: 0.3771 (mtpt) REVERT: C 1294 GLU cc_start: 0.7235 (tp30) cc_final: 0.6803 (tt0) REVERT: C 1351 MET cc_start: 0.6194 (mmt) cc_final: 0.5744 (mmm) REVERT: C 1405 MET cc_start: 0.7312 (ptp) cc_final: 0.6897 (ptp) REVERT: C 1726 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6232 (mtt) REVERT: C 1727 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6873 (mm) REVERT: C 1987 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: C 2026 GLU cc_start: 0.6811 (pp20) cc_final: 0.6422 (pt0) REVERT: C 2049 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8469 (pt) REVERT: C 2218 MET cc_start: 0.7015 (tpt) cc_final: 0.6612 (mmp) REVERT: C 2347 PHE cc_start: 0.7172 (p90) cc_final: 0.6837 (p90) outliers start: 129 outliers final: 93 residues processed: 433 average time/residue: 0.2102 time to fit residues: 150.9245 Evaluate side-chains 437 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 326 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1165 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1402 ASP Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1701 PHE Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2147 THR Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2184 VAL Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2404 VAL Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 957 HIS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1165 PHE Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1188 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1315 ARG Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1402 ASP Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1688 THR Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1881 MET Chi-restraints excluded: chain B residue 1883 LEU Chi-restraints excluded: chain B residue 1970 MET Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2049 ILE Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2147 THR Chi-restraints excluded: chain B residue 2242 ILE Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 957 HIS Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1017 MET Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1165 PHE Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1199 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 THR Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1235 ILE Chi-restraints excluded: chain C residue 1295 THR Chi-restraints excluded: chain C residue 1315 ARG Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1667 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1726 MET Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1960 ILE Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2099 SER Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2147 THR Chi-restraints excluded: chain C residue 2242 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 349 optimal weight: 3.9990 chunk 378 optimal weight: 1.9990 chunk 147 optimal weight: 0.0470 chunk 397 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 3 optimal weight: 0.1980 chunk 394 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1034 ASN A1131 ASN ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1904 GLN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS B1131 ASN C1131 ASN C2206 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.188720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.154518 restraints weight = 61455.182| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.76 r_work: 0.3722 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33960 Z= 0.128 Angle : 0.644 15.228 46059 Z= 0.332 Chirality : 0.044 0.310 5139 Planarity : 0.005 0.077 5736 Dihedral : 4.933 43.001 4442 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.96 % Favored : 92.14 % Rotamer: Outliers : 2.99 % Allowed : 23.75 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.01 (0.13), residues: 4035 helix: 1.18 (0.10), residues: 2499 sheet: 0.56 (0.33), residues: 237 loop : -2.58 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B1366 TYR 0.051 0.001 TYR A 953 PHE 0.053 0.001 PHE B 825 TRP 0.020 0.001 TRP B1077 HIS 0.004 0.001 HIS A1219 Details of bonding type rmsd covalent geometry : bond 0.00279 (33957) covalent geometry : angle 0.64397 (46053) SS BOND : bond 0.00062 ( 3) SS BOND : angle 1.62220 ( 6) hydrogen bonds : bond 0.04022 ( 1917) hydrogen bonds : angle 4.65173 ( 5697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8070 Ramachandran restraints generated. 4035 Oldfield, 0 Emsley, 4035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 342 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 887 MET cc_start: 0.3052 (mmm) cc_final: 0.2316 (mtt) REVERT: A 1210 MET cc_start: 0.2922 (ppp) cc_final: 0.1483 (tpt) REVERT: A 1222 LYS cc_start: 0.4285 (OUTLIER) cc_final: 0.3557 (mtpt) REVERT: A 1260 LYS cc_start: 0.7573 (tttt) cc_final: 0.6828 (tptp) REVERT: A 1276 ASN cc_start: 0.7844 (t0) cc_final: 0.7598 (t0) REVERT: A 1294 GLU cc_start: 0.7334 (tp30) cc_final: 0.7040 (tt0) REVERT: A 1628 MET cc_start: 0.8204 (mmt) cc_final: 0.7955 (mmm) REVERT: A 2113 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: A 2231 ASP cc_start: 0.6716 (m-30) cc_final: 0.6376 (m-30) REVERT: A 2255 THR cc_start: 0.8613 (m) cc_final: 0.8406 (p) REVERT: A 2347 PHE cc_start: 0.7344 (p90) cc_final: 0.7017 (p90) REVERT: B 875 MET cc_start: 0.4638 (ptt) cc_final: 0.3950 (tpt) REVERT: B 887 MET cc_start: 0.2539 (mmm) cc_final: 0.2167 (mtt) REVERT: B 957 HIS cc_start: -0.0411 (OUTLIER) cc_final: -0.0640 (m90) REVERT: B 983 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5267 (tmm160) REVERT: B 1006 MET cc_start: 0.5513 (tpp) cc_final: 0.5290 (tpp) REVERT: B 1086 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7531 (ptt-90) REVERT: B 1188 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6051 (tt) REVERT: B 1200 MET cc_start: 0.6718 (tpp) cc_final: 0.6349 (tpp) REVERT: B 1210 MET cc_start: 0.2536 (ppp) cc_final: 0.1149 (tpt) REVERT: B 1222 LYS cc_start: 0.4291 (OUTLIER) cc_final: 0.3864 (mtpt) REVERT: B 1235 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5279 (tt) REVERT: B 1294 GLU cc_start: 0.7399 (tp30) cc_final: 0.6993 (tt0) REVERT: B 1392 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6869 (p) REVERT: B 1405 MET cc_start: 0.7210 (ptp) cc_final: 0.6943 (ptp) REVERT: B 1701 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8172 (t80) REVERT: B 1727 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6442 (mm) REVERT: B 2082 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.6956 (mtm-85) REVERT: B 2231 ASP cc_start: 0.6753 (m-30) cc_final: 0.6333 (m-30) REVERT: B 2284 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7688 (mtt180) REVERT: B 2347 PHE cc_start: 0.7466 (p90) cc_final: 0.7172 (p90) REVERT: C 858 SER cc_start: 0.7430 (OUTLIER) cc_final: 0.7083 (p) REVERT: C 875 MET cc_start: 0.3566 (ptt) cc_final: 0.3243 (tpt) REVERT: C 1205 ASN cc_start: 0.4100 (t0) cc_final: 0.3737 (m110) REVERT: C 1210 MET cc_start: 0.2175 (ppp) cc_final: 0.0854 (tpt) REVERT: C 1222 LYS cc_start: 0.4303 (OUTLIER) cc_final: 0.3790 (mtpt) REVERT: C 1294 GLU cc_start: 0.7401 (tp30) cc_final: 0.6793 (tt0) REVERT: C 1351 MET cc_start: 0.6215 (mmt) cc_final: 0.5755 (mmm) REVERT: C 1405 MET cc_start: 0.7312 (ptp) cc_final: 0.6909 (ptp) REVERT: C 1726 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6158 (mtt) REVERT: C 1727 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6882 (mm) REVERT: C 1987 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: C 2049 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8454 (pt) REVERT: C 2218 MET cc_start: 0.7003 (tpt) cc_final: 0.6608 (mmp) REVERT: C 2347 PHE cc_start: 0.7142 (p90) cc_final: 0.6833 (p90) outliers start: 108 outliers final: 84 residues processed: 431 average time/residue: 0.2150 time to fit residues: 151.6305 Evaluate side-chains 431 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 331 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1027 TRP Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1165 PHE Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1249 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1402 ASP Chi-restraints excluded: chain A residue 1667 VAL Chi-restraints excluded: chain A residue 1676 PHE Chi-restraints excluded: chain A residue 1697 LEU Chi-restraints excluded: chain A residue 1819 GLN Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 2059 SER Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2113 GLN Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2184 VAL Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2299 SER Chi-restraints excluded: chain A residue 2404 VAL Chi-restraints excluded: chain A residue 2421 ILE Chi-restraints excluded: chain A residue 2433 TRP Chi-restraints excluded: chain B residue 957 HIS Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1017 MET Chi-restraints excluded: chain B residue 1027 TRP Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1131 ASN Chi-restraints excluded: chain B residue 1165 PHE Chi-restraints excluded: chain B residue 1178 THR Chi-restraints excluded: chain B residue 1188 LEU Chi-restraints excluded: chain B residue 1201 LEU Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1222 LYS Chi-restraints excluded: chain B residue 1235 ILE Chi-restraints excluded: chain B residue 1268 LEU Chi-restraints excluded: chain B residue 1315 ARG Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 1370 GLU Chi-restraints excluded: chain B residue 1392 VAL Chi-restraints excluded: chain B residue 1667 VAL Chi-restraints excluded: chain B residue 1676 PHE Chi-restraints excluded: chain B residue 1701 PHE Chi-restraints excluded: chain B residue 1715 VAL Chi-restraints excluded: chain B residue 1727 LEU Chi-restraints excluded: chain B residue 1819 GLN Chi-restraints excluded: chain B residue 1883 LEU Chi-restraints excluded: chain B residue 1970 MET Chi-restraints excluded: chain B residue 1976 PHE Chi-restraints excluded: chain B residue 2045 MET Chi-restraints excluded: chain B residue 2063 LEU Chi-restraints excluded: chain B residue 2075 MET Chi-restraints excluded: chain B residue 2080 THR Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2255 THR Chi-restraints excluded: chain B residue 2272 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2421 ILE Chi-restraints excluded: chain B residue 2433 TRP Chi-restraints excluded: chain C residue 858 SER Chi-restraints excluded: chain C residue 1002 LEU Chi-restraints excluded: chain C residue 1027 TRP Chi-restraints excluded: chain C residue 1131 ASN Chi-restraints excluded: chain C residue 1165 PHE Chi-restraints excluded: chain C residue 1178 THR Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1220 THR Chi-restraints excluded: chain C residue 1222 LYS Chi-restraints excluded: chain C residue 1235 ILE Chi-restraints excluded: chain C residue 1295 THR Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1370 GLU Chi-restraints excluded: chain C residue 1667 VAL Chi-restraints excluded: chain C residue 1676 PHE Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1701 PHE Chi-restraints excluded: chain C residue 1726 MET Chi-restraints excluded: chain C residue 1727 LEU Chi-restraints excluded: chain C residue 1819 GLN Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1976 PHE Chi-restraints excluded: chain C residue 1987 GLU Chi-restraints excluded: chain C residue 2049 ILE Chi-restraints excluded: chain C residue 2059 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2099 SER Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2242 ILE Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2421 ILE Chi-restraints excluded: chain C residue 2433 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 274 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 199 optimal weight: 0.1980 chunk 285 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 226 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2206 HIS ** B1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.188731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153972 restraints weight = 61412.965| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.81 r_work: 0.3715 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 33960 Z= 0.204 Angle : 0.915 59.193 46059 Z= 0.519 Chirality : 0.045 0.475 5139 Planarity : 0.005 0.076 5736 Dihedral : 4.947 42.918 4442 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.86 % Favored : 92.24 % Rotamer: Outliers : 2.94 % Allowed : 23.91 % Favored : 73.15 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.02 (0.13), residues: 4035 helix: 1.17 (0.10), residues: 2499 sheet: 0.56 (0.33), residues: 237 loop : -2.57 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1366 TYR 0.094 0.002 TYR C 953 PHE 0.053 0.001 PHE C1000 TRP 0.019 0.001 TRP B1077 HIS 0.015 0.001 HIS C 957 Details of bonding type rmsd covalent geometry : bond 0.00391 (33957) covalent geometry : angle 0.91465 (46053) SS BOND : bond 0.00090 ( 3) SS BOND : angle 1.59998 ( 6) hydrogen bonds : bond 0.04043 ( 1917) hydrogen bonds : angle 4.65690 ( 5697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10063.48 seconds wall clock time: 172 minutes 39.32 seconds (10359.32 seconds total)