Starting phenix.real_space_refine on Tue Aug 26 19:01:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl2_38435/08_2025/8xl2_38435.map" } resolution = 2.73 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= -0.001 sd= 0.078 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 225 5.16 5 C 25138 2.51 5 N 6859 2.21 5 O 7325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39556 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 12307 Classifications: {'peptide': 1527} Link IDs: {'PTRANS': 64, 'TRANS': 1462} Chain breaks: 5 Chain: "B" Number of atoms: 12307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 12307 Classifications: {'peptide': 1527} Link IDs: {'PTRANS': 64, 'TRANS': 1462} Chain breaks: 5 Chain: "D" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4365 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain: "C" Number of atoms: 10424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1300, 10424 Classifications: {'peptide': 1300} Link IDs: {'PTRANS': 56, 'TRANS': 1243} Chain breaks: 5 Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'ACO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.52, per 1000 atoms: 0.24 Number of scatterers: 39556 At special positions: 0 Unit cell: (136.817, 143.281, 353.354, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 225 16.00 P 9 15.00 O 7325 8.00 N 6859 7.00 C 25138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9240 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 32 sheets defined 47.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 627 through 658 removed outlier: 3.643A pdb=" N GLY A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 865 removed outlier: 3.797A pdb=" N HIS A 854 " --> pdb=" O HIS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 891 Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 911 through 928 Processing helix chain 'A' and resid 937 through 952 Processing helix chain 'A' and resid 957 through 964 removed outlier: 3.687A pdb=" N PHE A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 975 Processing helix chain 'A' and resid 977 through 999 removed outlier: 3.538A pdb=" N VAL A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1021 through 1033 removed outlier: 3.979A pdb=" N GLN A1033 " --> pdb=" O PHE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 3.674A pdb=" N GLN A1047 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A1049 " --> pdb=" O ILE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1068 Processing helix chain 'A' and resid 1071 through 1073 No H-bonds generated for 'chain 'A' and resid 1071 through 1073' Processing helix chain 'A' and resid 1074 through 1088 Processing helix chain 'A' and resid 1093 through 1107 removed outlier: 3.588A pdb=" N ALA A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1133 through 1137 Processing helix chain 'A' and resid 1144 through 1158 removed outlier: 3.526A pdb=" N ALA A1148 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1248 removed outlier: 4.030A pdb=" N VAL A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1253 Processing helix chain 'A' and resid 1300 through 1313 removed outlier: 3.916A pdb=" N PHE A1311 " --> pdb=" O MET A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1321 Processing helix chain 'A' and resid 1438 through 1464 removed outlier: 3.922A pdb=" N LEU A1442 " --> pdb=" O SER A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1498 Processing helix chain 'A' and resid 1499 through 1506 Processing helix chain 'A' and resid 1585 through 1592 Processing helix chain 'A' and resid 1597 through 1599 No H-bonds generated for 'chain 'A' and resid 1597 through 1599' Processing helix chain 'A' and resid 1600 through 1616 removed outlier: 3.723A pdb=" N MET A1604 " --> pdb=" O ASP A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1619 No H-bonds generated for 'chain 'A' and resid 1617 through 1619' Processing helix chain 'A' and resid 1692 through 1710 Processing helix chain 'A' and resid 1727 through 1733 Processing helix chain 'A' and resid 1743 through 1746 Processing helix chain 'A' and resid 1754 through 1759 Processing helix chain 'A' and resid 1761 through 1765 Processing helix chain 'A' and resid 1794 through 1812 removed outlier: 3.942A pdb=" N ASN A1812 " --> pdb=" O SER A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1836 removed outlier: 3.781A pdb=" N VAL A1832 " --> pdb=" O GLY A1828 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1859 Processing helix chain 'A' and resid 1866 through 1871 Processing helix chain 'A' and resid 1871 through 1876 Processing helix chain 'A' and resid 1887 through 1901 removed outlier: 3.505A pdb=" N GLY A1891 " --> pdb=" O ASP A1887 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A1901 " --> pdb=" O HIS A1897 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1938 Processing helix chain 'A' and resid 2019 through 2037 removed outlier: 3.507A pdb=" N GLY A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2058 Processing helix chain 'A' and resid 2060 through 2073 removed outlier: 3.858A pdb=" N VAL A2068 " --> pdb=" O GLY A2064 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A2073 " --> pdb=" O ASP A2069 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2097 removed outlier: 3.837A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2101 Processing helix chain 'A' and resid 2119 through 2128 removed outlier: 3.628A pdb=" N THR A2123 " --> pdb=" O GLU A2119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A2126 " --> pdb=" O GLY A2122 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2138 Processing helix chain 'A' and resid 2141 through 2152 Processing helix chain 'A' and resid 2157 through 2175 removed outlier: 3.755A pdb=" N ARG A2161 " --> pdb=" O SER A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2192 through 2200 removed outlier: 3.722A pdb=" N MET A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2210 through 2236 removed outlier: 3.542A pdb=" N PHE A2214 " --> pdb=" O THR A2210 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP A2217 " --> pdb=" O THR A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2257 Processing helix chain 'A' and resid 2266 through 2280 Processing helix chain 'A' and resid 2286 through 2311 Processing helix chain 'A' and resid 2314 through 2322 removed outlier: 3.894A pdb=" N ILE A2320 " --> pdb=" O MET A2316 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A2321 " --> pdb=" O ASP A2317 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A2322 " --> pdb=" O SER A2318 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2337 Processing helix chain 'B' and resid 627 through 658 removed outlier: 3.642A pdb=" N GLY B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 865 removed outlier: 3.797A pdb=" N HIS B 854 " --> pdb=" O HIS B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 891 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 911 through 928 Processing helix chain 'B' and resid 937 through 952 Processing helix chain 'B' and resid 957 through 964 removed outlier: 3.687A pdb=" N PHE B 961 " --> pdb=" O GLU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 975 Processing helix chain 'B' and resid 977 through 999 removed outlier: 3.538A pdb=" N VAL B 987 " --> pdb=" O MET B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1017 Processing helix chain 'B' and resid 1021 through 1033 removed outlier: 3.979A pdb=" N GLN B1033 " --> pdb=" O PHE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1049 removed outlier: 3.675A pdb=" N GLN B1047 " --> pdb=" O MET B1043 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B1049 " --> pdb=" O ILE B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1068 Processing helix chain 'B' and resid 1071 through 1073 No H-bonds generated for 'chain 'B' and resid 1071 through 1073' Processing helix chain 'B' and resid 1074 through 1088 Processing helix chain 'B' and resid 1093 through 1107 removed outlier: 3.588A pdb=" N ALA B1107 " --> pdb=" O ILE B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1126 Processing helix chain 'B' and resid 1133 through 1137 Processing helix chain 'B' and resid 1144 through 1158 removed outlier: 3.526A pdb=" N ALA B1148 " --> pdb=" O VAL B1144 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B1154 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1242 through 1248 removed outlier: 4.031A pdb=" N VAL B1246 " --> pdb=" O PHE B1242 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1253 Processing helix chain 'B' and resid 1300 through 1313 removed outlier: 3.916A pdb=" N PHE B1311 " --> pdb=" O MET B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1321 Processing helix chain 'B' and resid 1438 through 1464 removed outlier: 3.922A pdb=" N LEU B1442 " --> pdb=" O SER B1438 " (cutoff:3.500A) Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1499 through 1506 Processing helix chain 'B' and resid 1585 through 1592 Processing helix chain 'B' and resid 1597 through 1599 No H-bonds generated for 'chain 'B' and resid 1597 through 1599' Processing helix chain 'B' and resid 1600 through 1616 removed outlier: 3.723A pdb=" N MET B1604 " --> pdb=" O ASP B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1617 through 1619 No H-bonds generated for 'chain 'B' and resid 1617 through 1619' Processing helix chain 'B' and resid 1692 through 1710 Processing helix chain 'B' and resid 1727 through 1733 Processing helix chain 'B' and resid 1743 through 1746 Processing helix chain 'B' and resid 1754 through 1759 Processing helix chain 'B' and resid 1761 through 1765 Processing helix chain 'B' and resid 1794 through 1812 removed outlier: 3.848A pdb=" N ASN B1812 " --> pdb=" O SER B1808 " (cutoff:3.500A) Processing helix chain 'B' and resid 1826 through 1836 removed outlier: 3.782A pdb=" N VAL B1832 " --> pdb=" O GLY B1828 " (cutoff:3.500A) Processing helix chain 'B' and resid 1850 through 1859 Processing helix chain 'B' and resid 1866 through 1871 Processing helix chain 'B' and resid 1871 through 1876 Processing helix chain 'B' and resid 1887 through 1901 removed outlier: 3.505A pdb=" N GLY B1891 " --> pdb=" O ASP B1887 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR B1901 " --> pdb=" O HIS B1897 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1938 Processing helix chain 'B' and resid 2019 through 2037 removed outlier: 3.506A pdb=" N GLY B2037 " --> pdb=" O PHE B2033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2052 through 2058 Processing helix chain 'B' and resid 2060 through 2073 removed outlier: 3.858A pdb=" N VAL B2068 " --> pdb=" O GLY B2064 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU B2073 " --> pdb=" O ASP B2069 " (cutoff:3.500A) Processing helix chain 'B' and resid 2092 through 2097 removed outlier: 3.836A pdb=" N ILE B2096 " --> pdb=" O SER B2092 " (cutoff:3.500A) Processing helix chain 'B' and resid 2098 through 2101 Processing helix chain 'B' and resid 2119 through 2128 removed outlier: 3.795A pdb=" N ILE B2126 " --> pdb=" O GLY B2122 " (cutoff:3.500A) Processing helix chain 'B' and resid 2129 through 2138 Processing helix chain 'B' and resid 2141 through 2152 Processing helix chain 'B' and resid 2157 through 2174 removed outlier: 3.754A pdb=" N ARG B2161 " --> pdb=" O SER B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2175 through 2189 removed outlier: 3.587A pdb=" N TYR B2179 " --> pdb=" O LEU B2175 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2200 removed outlier: 3.721A pdb=" N MET B2196 " --> pdb=" O THR B2192 " (cutoff:3.500A) Processing helix chain 'B' and resid 2210 through 2236 removed outlier: 3.543A pdb=" N PHE B2214 " --> pdb=" O THR B2210 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP B2217 " --> pdb=" O THR B2213 " (cutoff:3.500A) Processing helix chain 'B' and resid 2240 through 2257 Processing helix chain 'B' and resid 2266 through 2280 Processing helix chain 'B' and resid 2286 through 2311 Processing helix chain 'B' and resid 2314 through 2322 removed outlier: 3.894A pdb=" N ILE B2320 " --> pdb=" O MET B2316 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS B2321 " --> pdb=" O ASP B2317 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET B2322 " --> pdb=" O SER B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2327 through 2337 Processing helix chain 'D' and resid 1794 through 1812 removed outlier: 3.943A pdb=" N ASN D1812 " --> pdb=" O SER D1808 " (cutoff:3.500A) Processing helix chain 'D' and resid 1826 through 1836 removed outlier: 3.781A pdb=" N VAL D1832 " --> pdb=" O GLY D1828 " (cutoff:3.500A) Processing helix chain 'D' and resid 1850 through 1859 Processing helix chain 'D' and resid 1866 through 1871 Processing helix chain 'D' and resid 1871 through 1876 Processing helix chain 'D' and resid 1887 through 1901 removed outlier: 3.505A pdb=" N GLY D1891 " --> pdb=" O ASP D1887 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR D1901 " --> pdb=" O HIS D1897 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1938 Processing helix chain 'D' and resid 2019 through 2037 removed outlier: 3.507A pdb=" N GLY D2037 " --> pdb=" O PHE D2033 " (cutoff:3.500A) Processing helix chain 'D' and resid 2052 through 2058 Processing helix chain 'D' and resid 2060 through 2073 removed outlier: 3.859A pdb=" N VAL D2068 " --> pdb=" O GLY D2064 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D2073 " --> pdb=" O ASP D2069 " (cutoff:3.500A) Processing helix chain 'D' and resid 2092 through 2097 removed outlier: 3.836A pdb=" N ILE D2096 " --> pdb=" O SER D2092 " (cutoff:3.500A) Processing helix chain 'D' and resid 2098 through 2101 Processing helix chain 'D' and resid 2119 through 2128 removed outlier: 3.794A pdb=" N ILE D2126 " --> pdb=" O GLY D2122 " (cutoff:3.500A) Processing helix chain 'D' and resid 2129 through 2138 Processing helix chain 'D' and resid 2141 through 2152 Processing helix chain 'D' and resid 2157 through 2175 removed outlier: 3.754A pdb=" N ARG D2161 " --> pdb=" O SER D2157 " (cutoff:3.500A) Processing helix chain 'D' and resid 2175 through 2189 Processing helix chain 'D' and resid 2192 through 2200 removed outlier: 3.722A pdb=" N MET D2196 " --> pdb=" O THR D2192 " (cutoff:3.500A) Processing helix chain 'D' and resid 2210 through 2236 removed outlier: 3.543A pdb=" N PHE D2214 " --> pdb=" O THR D2210 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP D2217 " --> pdb=" O THR D2213 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2257 Processing helix chain 'D' and resid 2266 through 2280 Processing helix chain 'D' and resid 2286 through 2311 Processing helix chain 'D' and resid 2314 through 2322 removed outlier: 3.893A pdb=" N ILE D2320 " --> pdb=" O MET D2316 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS D2321 " --> pdb=" O ASP D2317 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D2322 " --> pdb=" O SER D2318 " (cutoff:3.500A) Processing helix chain 'D' and resid 2327 through 2337 Processing helix chain 'C' and resid 627 through 658 removed outlier: 3.642A pdb=" N GLY C 658 " --> pdb=" O SER C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 865 removed outlier: 3.797A pdb=" N HIS C 854 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 891 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 911 through 928 Processing helix chain 'C' and resid 937 through 952 Processing helix chain 'C' and resid 957 through 964 removed outlier: 3.687A pdb=" N PHE C 961 " --> pdb=" O GLU C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 975 Processing helix chain 'C' and resid 977 through 999 removed outlier: 3.538A pdb=" N VAL C 987 " --> pdb=" O MET C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1017 Processing helix chain 'C' and resid 1021 through 1033 removed outlier: 3.979A pdb=" N GLN C1033 " --> pdb=" O PHE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1049 removed outlier: 3.675A pdb=" N GLN C1047 " --> pdb=" O MET C1043 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C1049 " --> pdb=" O ILE C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1068 Processing helix chain 'C' and resid 1071 through 1073 No H-bonds generated for 'chain 'C' and resid 1071 through 1073' Processing helix chain 'C' and resid 1074 through 1088 Processing helix chain 'C' and resid 1093 through 1107 removed outlier: 3.587A pdb=" N ALA C1107 " --> pdb=" O ILE C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1126 Processing helix chain 'C' and resid 1133 through 1137 Processing helix chain 'C' and resid 1144 through 1158 removed outlier: 3.526A pdb=" N ALA C1148 " --> pdb=" O VAL C1144 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C1154 " --> pdb=" O LEU C1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1248 removed outlier: 4.031A pdb=" N VAL C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1253 Processing helix chain 'C' and resid 1300 through 1313 removed outlier: 3.917A pdb=" N PHE C1311 " --> pdb=" O MET C1307 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1321 Processing helix chain 'C' and resid 1438 through 1464 removed outlier: 3.921A pdb=" N LEU C1442 " --> pdb=" O SER C1438 " (cutoff:3.500A) Processing helix chain 'C' and resid 1484 through 1498 Processing helix chain 'C' and resid 1499 through 1506 Processing helix chain 'C' and resid 1585 through 1592 Processing helix chain 'C' and resid 1597 through 1599 No H-bonds generated for 'chain 'C' and resid 1597 through 1599' Processing helix chain 'C' and resid 1600 through 1616 removed outlier: 3.723A pdb=" N MET C1604 " --> pdb=" O ASP C1600 " (cutoff:3.500A) Processing helix chain 'C' and resid 1617 through 1619 No H-bonds generated for 'chain 'C' and resid 1617 through 1619' Processing helix chain 'C' and resid 1692 through 1710 Processing helix chain 'C' and resid 1727 through 1733 Processing helix chain 'C' and resid 1743 through 1746 Processing helix chain 'C' and resid 1754 through 1759 Processing helix chain 'C' and resid 1761 through 1765 Processing helix chain 'C' and resid 1794 through 1812 removed outlier: 3.848A pdb=" N ASN C1812 " --> pdb=" O SER C1808 " (cutoff:3.500A) Processing helix chain 'C' and resid 1826 through 1836 removed outlier: 3.782A pdb=" N VAL C1832 " --> pdb=" O GLY C1828 " (cutoff:3.500A) Processing helix chain 'C' and resid 1850 through 1859 Processing helix chain 'C' and resid 1866 through 1871 Processing helix chain 'C' and resid 1871 through 1876 Processing helix chain 'C' and resid 1887 through 1901 removed outlier: 3.504A pdb=" N GLY C1891 " --> pdb=" O ASP C1887 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C1901 " --> pdb=" O HIS C1897 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1938 Processing helix chain 'C' and resid 2019 through 2037 removed outlier: 3.506A pdb=" N GLY C2037 " --> pdb=" O PHE C2033 " (cutoff:3.500A) Processing helix chain 'C' and resid 2052 through 2058 Processing helix chain 'C' and resid 2060 through 2073 removed outlier: 3.858A pdb=" N VAL C2068 " --> pdb=" O GLY C2064 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C2073 " --> pdb=" O ASP C2069 " (cutoff:3.500A) Processing helix chain 'C' and resid 2089 through 2091 No H-bonds generated for 'chain 'C' and resid 2089 through 2091' Processing helix chain 'C' and resid 2092 through 2097 removed outlier: 3.836A pdb=" N ILE C2096 " --> pdb=" O SER C2092 " (cutoff:3.500A) Processing helix chain 'C' and resid 2098 through 2101 Processing sheet with id=AA1, first strand: chain 'A' and resid 669 through 676 Processing sheet with id=AA2, first strand: chain 'A' and resid 1162 through 1170 removed outlier: 6.610A pdb=" N GLN A1181 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A1166 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU A1179 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A1168 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1177 " --> pdb=" O HIS A1168 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N CYS A1176 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A1238 " --> pdb=" O CYS A1176 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET A1233 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN A1290 " --> pdb=" O MET A1233 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A1235 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA A1292 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1237 " --> pdb=" O ALA A1292 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS A1287 " --> pdb=" O ARG A1326 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR A1328 " --> pdb=" O HIS A1287 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A1289 " --> pdb=" O THR A1328 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A1330 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1291 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1389 through 1393 removed outlier: 8.564A pdb=" N HIS A1472 " --> pdb=" O TYR A1419 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A1421 " --> pdb=" O HIS A1472 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE A1474 " --> pdb=" O PHE A1421 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A1423 " --> pdb=" O PHE A1474 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASN A1476 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA A1425 " --> pdb=" O ASN A1476 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A1478 " --> pdb=" O ALA A1425 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE A1427 " --> pdb=" O VAL A1478 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR A1480 " --> pdb=" O ILE A1427 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN A1471 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN A1516 " --> pdb=" O PHE A1477 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A1509 " --> pdb=" O ASN A1534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1645 through 1648 removed outlier: 4.438A pdb=" N ALA A1661 " --> pdb=" O LEU A1637 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A1639 " --> pdb=" O MET A1659 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N MET A1659 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE A1714 " --> pdb=" O ASP A1676 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A1678 " --> pdb=" O ILE A1714 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A1716 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A1680 " --> pdb=" O VAL A1716 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ILE A1839 " --> pdb=" O THR A1816 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A1818 " --> pdb=" O ILE A1839 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A1841 " --> pdb=" O SER A1818 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A1820 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A1883 " --> pdb=" O THR A1838 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1735 through 1738 removed outlier: 6.366A pdb=" N HIS A1735 " --> pdb=" O LEU A1751 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A1751 " --> pdb=" O HIS A1735 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA A1737 " --> pdb=" O ARG A1749 " (cutoff:3.500A) removed outlier: 16.928A pdb=" N ARG A1749 " --> pdb=" O ASP A1784 " (cutoff:3.500A) removed outlier: 12.397A pdb=" N ASP A1784 " --> pdb=" O ARG A1749 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A1751 " --> pdb=" O ILE A1782 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER A1778 " --> pdb=" O ASP A1774 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP A1774 " --> pdb=" O SER A1778 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR A1780 " --> pdb=" O VAL A1772 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1772 " --> pdb=" O TYR A1780 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE A1782 " --> pdb=" O GLU A1770 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU A1770 " --> pdb=" O ILE A1782 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1824 through 1825 removed outlier: 6.421A pdb=" N ALA A1824 " --> pdb=" O ILE A1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1961 through 1962 removed outlier: 7.918A pdb=" N MET A2041 " --> pdb=" O PRO A1982 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY A1984 " --> pdb=" O MET A2041 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE A2043 " --> pdb=" O GLY A1984 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A1986 " --> pdb=" O PHE A2043 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A2040 " --> pdb=" O LEU A2079 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A2081 " --> pdb=" O LEU A2040 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A2042 " --> pdb=" O TYR A2081 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A2206 " --> pdb=" O MET A2107 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA A2109 " --> pdb=" O LEU A2206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1993 through 1997 Processing sheet with id=AA9, first strand: chain 'A' and resid 2017 through 2018 Processing sheet with id=AB1, first strand: chain 'A' and resid 2086 through 2089 Processing sheet with id=AB2, first strand: chain 'B' and resid 669 through 676 Processing sheet with id=AB3, first strand: chain 'B' and resid 1162 through 1170 removed outlier: 6.610A pdb=" N GLN B1181 " --> pdb=" O ASN B1164 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL B1166 " --> pdb=" O GLU B1179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B1179 " --> pdb=" O VAL B1166 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HIS B1168 " --> pdb=" O VAL B1177 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1177 " --> pdb=" O HIS B1168 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N CYS B1176 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B1238 " --> pdb=" O CYS B1176 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET B1233 " --> pdb=" O ILE B1288 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN B1290 " --> pdb=" O MET B1233 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY B1235 " --> pdb=" O ASN B1290 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA B1292 " --> pdb=" O GLY B1235 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B1237 " --> pdb=" O ALA B1292 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS B1287 " --> pdb=" O ARG B1326 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR B1328 " --> pdb=" O HIS B1287 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B1289 " --> pdb=" O THR B1328 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU B1330 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1291 " --> pdb=" O LEU B1330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1389 through 1393 removed outlier: 8.565A pdb=" N HIS B1472 " --> pdb=" O TYR B1419 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B1421 " --> pdb=" O HIS B1472 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE B1474 " --> pdb=" O PHE B1421 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B1423 " --> pdb=" O PHE B1474 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASN B1476 " --> pdb=" O VAL B1423 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA B1425 " --> pdb=" O ASN B1476 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B1478 " --> pdb=" O ALA B1425 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE B1427 " --> pdb=" O VAL B1478 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR B1480 " --> pdb=" O ILE B1427 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASN B1471 " --> pdb=" O VAL B1508 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN B1516 " --> pdb=" O PHE B1477 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B1509 " --> pdb=" O ASN B1534 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1645 through 1648 removed outlier: 4.438A pdb=" N ALA B1661 " --> pdb=" O LEU B1637 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU B1639 " --> pdb=" O MET B1659 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N MET B1659 " --> pdb=" O LEU B1639 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ILE B1714 " --> pdb=" O ASP B1676 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B1678 " --> pdb=" O ILE B1714 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL B1716 " --> pdb=" O ILE B1678 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B1680 " --> pdb=" O VAL B1716 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE B1839 " --> pdb=" O THR B1816 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B1818 " --> pdb=" O ILE B1839 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL B1841 " --> pdb=" O SER B1818 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B1820 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS B1883 " --> pdb=" O THR B1838 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1735 through 1738 removed outlier: 6.365A pdb=" N HIS B1735 " --> pdb=" O LEU B1751 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B1751 " --> pdb=" O HIS B1735 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B1737 " --> pdb=" O ARG B1749 " (cutoff:3.500A) removed outlier: 16.928A pdb=" N ARG B1749 " --> pdb=" O ASP B1784 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N ASP B1784 " --> pdb=" O ARG B1749 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU B1751 " --> pdb=" O ILE B1782 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER B1778 " --> pdb=" O ASP B1774 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP B1774 " --> pdb=" O SER B1778 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR B1780 " --> pdb=" O VAL B1772 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B1772 " --> pdb=" O TYR B1780 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE B1782 " --> pdb=" O GLU B1770 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU B1770 " --> pdb=" O ILE B1782 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1824 through 1825 removed outlier: 6.422A pdb=" N ALA B1824 " --> pdb=" O ILE B1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1961 through 1962 removed outlier: 7.918A pdb=" N MET B2041 " --> pdb=" O PRO B1982 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY B1984 " --> pdb=" O MET B2041 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE B2043 " --> pdb=" O GLY B1984 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1986 " --> pdb=" O PHE B2043 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B2040 " --> pdb=" O LEU B2079 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N TYR B2081 " --> pdb=" O LEU B2040 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B2042 " --> pdb=" O TYR B2081 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU B2206 " --> pdb=" O MET B2107 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA B2109 " --> pdb=" O LEU B2206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1993 through 1997 Processing sheet with id=AC1, first strand: chain 'B' and resid 2086 through 2089 removed outlier: 6.463A pdb=" N ALA B2086 " --> pdb=" O ARG B2114 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER B2116 " --> pdb=" O ALA B2086 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B2088 " --> pdb=" O SER B2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1818 through 1820 removed outlier: 6.491A pdb=" N SER D1818 " --> pdb=" O ILE D1839 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL D1841 " --> pdb=" O SER D1818 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D1820 " --> pdb=" O VAL D1841 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D1883 " --> pdb=" O THR D1838 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1824 through 1825 removed outlier: 6.421A pdb=" N ALA D1824 " --> pdb=" O ILE D1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 1961 through 1962 removed outlier: 7.918A pdb=" N MET D2041 " --> pdb=" O PRO D1982 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY D1984 " --> pdb=" O MET D2041 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE D2043 " --> pdb=" O GLY D1984 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D1986 " --> pdb=" O PHE D2043 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D2040 " --> pdb=" O LEU D2079 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR D2081 " --> pdb=" O LEU D2040 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL D2042 " --> pdb=" O TYR D2081 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU D2206 " --> pdb=" O MET D2107 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA D2109 " --> pdb=" O LEU D2206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1993 through 1997 Processing sheet with id=AC6, first strand: chain 'D' and resid 2086 through 2089 removed outlier: 6.462A pdb=" N ALA D2086 " --> pdb=" O ARG D2114 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER D2116 " --> pdb=" O ALA D2086 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU D2088 " --> pdb=" O SER D2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 669 through 676 Processing sheet with id=AC8, first strand: chain 'C' and resid 1162 through 1170 removed outlier: 6.610A pdb=" N GLN C1181 " --> pdb=" O ASN C1164 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL C1166 " --> pdb=" O GLU C1179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU C1179 " --> pdb=" O VAL C1166 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS C1168 " --> pdb=" O VAL C1177 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C1177 " --> pdb=" O HIS C1168 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS C1176 " --> pdb=" O SER C1238 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER C1238 " --> pdb=" O CYS C1176 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET C1233 " --> pdb=" O ILE C1288 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN C1290 " --> pdb=" O MET C1233 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C1235 " --> pdb=" O ASN C1290 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA C1292 " --> pdb=" O GLY C1235 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C1237 " --> pdb=" O ALA C1292 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS C1287 " --> pdb=" O ARG C1326 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR C1328 " --> pdb=" O HIS C1287 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C1289 " --> pdb=" O THR C1328 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU C1330 " --> pdb=" O LEU C1289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C1291 " --> pdb=" O LEU C1330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1389 through 1393 removed outlier: 8.565A pdb=" N HIS C1472 " --> pdb=" O TYR C1419 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE C1421 " --> pdb=" O HIS C1472 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE C1474 " --> pdb=" O PHE C1421 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C1423 " --> pdb=" O PHE C1474 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASN C1476 " --> pdb=" O VAL C1423 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA C1425 " --> pdb=" O ASN C1476 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL C1478 " --> pdb=" O ALA C1425 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE C1427 " --> pdb=" O VAL C1478 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR C1480 " --> pdb=" O ILE C1427 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN C1471 " --> pdb=" O VAL C1508 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN C1516 " --> pdb=" O PHE C1477 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C1509 " --> pdb=" O ASN C1534 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1645 through 1648 removed outlier: 4.438A pdb=" N ALA C1661 " --> pdb=" O LEU C1637 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU C1639 " --> pdb=" O MET C1659 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N MET C1659 " --> pdb=" O LEU C1639 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ILE C1714 " --> pdb=" O ASP C1676 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C1678 " --> pdb=" O ILE C1714 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL C1716 " --> pdb=" O ILE C1678 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE C1680 " --> pdb=" O VAL C1716 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE C1839 " --> pdb=" O THR C1816 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C1818 " --> pdb=" O ILE C1839 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL C1841 " --> pdb=" O SER C1818 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C1820 " --> pdb=" O VAL C1841 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS C1883 " --> pdb=" O THR C1838 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1735 through 1738 removed outlier: 6.364A pdb=" N HIS C1735 " --> pdb=" O LEU C1751 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C1751 " --> pdb=" O HIS C1735 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA C1737 " --> pdb=" O ARG C1749 " (cutoff:3.500A) removed outlier: 16.929A pdb=" N ARG C1749 " --> pdb=" O ASP C1784 " (cutoff:3.500A) removed outlier: 12.398A pdb=" N ASP C1784 " --> pdb=" O ARG C1749 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU C1751 " --> pdb=" O ILE C1782 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C1778 " --> pdb=" O ASP C1774 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP C1774 " --> pdb=" O SER C1778 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR C1780 " --> pdb=" O VAL C1772 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C1772 " --> pdb=" O TYR C1780 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE C1782 " --> pdb=" O GLU C1770 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU C1770 " --> pdb=" O ILE C1782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1824 through 1825 removed outlier: 6.421A pdb=" N ALA C1824 " --> pdb=" O ILE C1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 1961 through 1962 removed outlier: 7.918A pdb=" N MET C2041 " --> pdb=" O PRO C1982 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY C1984 " --> pdb=" O MET C2041 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE C2043 " --> pdb=" O GLY C1984 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1986 " --> pdb=" O PHE C2043 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C2040 " --> pdb=" O LEU C2079 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR C2081 " --> pdb=" O LEU C2040 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL C2042 " --> pdb=" O TYR C2081 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1993 through 1997 1918 hydrogen bonds defined for protein. 5532 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: 11.66 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6563 1.31 - 1.44: 10698 1.44 - 1.56: 22737 1.56 - 1.69: 18 1.69 - 1.81: 382 Bond restraints: 40398 Sorted by residual: bond pdb=" C5A ACO A2501 " pdb=" C6A ACO A2501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5A ACO C2501 " pdb=" C6A ACO C2501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C5A ACO A2502 " pdb=" C6A ACO A2502 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C4A ACO A2501 " pdb=" C5A ACO A2501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.20e-02 6.94e+03 4.82e+01 bond pdb=" C4A ACO A2502 " pdb=" C5A ACO A2502 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.20e-02 6.94e+03 4.81e+01 ... (remaining 40393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 54228 3.27 - 6.54: 462 6.54 - 9.81: 31 9.81 - 13.08: 0 13.08 - 16.35: 6 Bond angle restraints: 54727 Sorted by residual: angle pdb=" P1A ACO A2501 " pdb=" O3A ACO A2501 " pdb=" P2A ACO A2501 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" P1A ACO C2501 " pdb=" O3A ACO C2501 " pdb=" P2A ACO C2501 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" P1A ACO A2502 " pdb=" O3A ACO A2502 " pdb=" P2A ACO A2502 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5A ACO C2501 " pdb=" C4A ACO C2501 " pdb=" N3A ACO C2501 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.65e+01 angle pdb=" C5A ACO A2502 " pdb=" C4A ACO A2502 " pdb=" N3A ACO A2502 " ideal model delta sigma weight residual 126.80 118.66 8.14 1.00e+00 1.00e+00 6.63e+01 ... (remaining 54722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 22866 17.66 - 35.33: 1239 35.33 - 52.99: 284 52.99 - 70.66: 63 70.66 - 88.32: 19 Dihedral angle restraints: 24471 sinusoidal: 10164 harmonic: 14307 Sorted by residual: dihedral pdb=" CA ARG C1687 " pdb=" C ARG C1687 " pdb=" N ILE C1688 " pdb=" CA ILE C1688 " ideal model delta harmonic sigma weight residual -180.00 -130.63 -49.37 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA ARG B1687 " pdb=" C ARG B1687 " pdb=" N ILE B1688 " pdb=" CA ILE B1688 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.73e+01 dihedral pdb=" CA ARG A1687 " pdb=" C ARG A1687 " pdb=" N ILE A1688 " pdb=" CA ILE A1688 " ideal model delta harmonic sigma weight residual 180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 ... (remaining 24468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4345 0.047 - 0.094: 1333 0.094 - 0.141: 362 0.141 - 0.188: 53 0.188 - 0.236: 5 Chirality restraints: 6098 Sorted by residual: chirality pdb=" CA VAL A2117 " pdb=" N VAL A2117 " pdb=" C VAL A2117 " pdb=" CB VAL A2117 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CAP ACO A2501 " pdb=" C9P ACO A2501 " pdb=" CBP ACO A2501 " pdb=" OAP ACO A2501 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CAP ACO A2502 " pdb=" C9P ACO A2502 " pdb=" CBP ACO A2502 " pdb=" OAP ACO A2502 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 6095 not shown) Planarity restraints: 7043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO C2501 " 0.350 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C9P ACO C2501 " -0.089 2.00e-02 2.50e+03 pdb=" CAP ACO C2501 " 0.164 2.00e-02 2.50e+03 pdb=" N8P ACO C2501 " -0.527 2.00e-02 2.50e+03 pdb=" O9P ACO C2501 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO A2502 " 0.348 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C9P ACO A2502 " -0.089 2.00e-02 2.50e+03 pdb=" CAP ACO A2502 " 0.167 2.00e-02 2.50e+03 pdb=" N8P ACO A2502 " -0.523 2.00e-02 2.50e+03 pdb=" O9P ACO A2502 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO A2501 " 0.301 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C5P ACO A2501 " -0.082 2.00e-02 2.50e+03 pdb=" C6P ACO A2501 " 0.189 2.00e-02 2.50e+03 pdb=" N4P ACO A2501 " -0.429 2.00e-02 2.50e+03 pdb=" O5P ACO A2501 " 0.020 2.00e-02 2.50e+03 ... (remaining 7040 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3386 2.74 - 3.28: 39273 3.28 - 3.82: 63584 3.82 - 4.36: 79149 4.36 - 4.90: 135149 Nonbonded interactions: 320541 Sorted by model distance: nonbonded pdb=" O VAL D1841 " pdb=" OG SER D1844 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A1841 " pdb=" OG SER A1844 " model vdw 2.201 3.040 nonbonded pdb=" O VAL C1841 " pdb=" OG SER C1844 " model vdw 2.201 3.040 nonbonded pdb=" O VAL B1841 " pdb=" OG SER B1844 " model vdw 2.201 3.040 nonbonded pdb=" O PHE D2174 " pdb=" OH TYR C1745 " model vdw 2.208 3.040 ... (remaining 320536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 619 through 2110) selection = (chain 'B' and resid 619 through 2110) selection = (chain 'C' and resid 619 through 2110) } 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: 8.070 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 41.450 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4065 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 : 0.007 0.102 40398 Z= 0.328 Angle : 0.809 16.351 54727 Z= 0.475 Chirality : 0.048 0.236 6098 Planarity : 0.008 0.299 7043 Dihedral : 12.318 88.322 15231 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.28 % Favored : 94.55 % Rotamer: Outliers : 1.70 % Allowed : 4.18 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.11), residues: 4863 helix: -0.79 (0.10), residues: 2034 sheet: -0.18 (0.15), residues: 890 loop : -2.00 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2212 TYR 0.015 0.002 TYR A1634 PHE 0.013 0.002 PHE C1691 TRP 0.019 0.002 TRP A2018 HIS 0.007 0.001 HIS D2190 Details of bonding type rmsd covalent geometry : bond 0.00700 (40398) covalent geometry : angle 0.80926 (54727) hydrogen bonds : bond 0.14719 ( 1918) hydrogen bonds : angle 6.85721 ( 5532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 764 time to evaluate : 1.588 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: symmetry clash REVERT: A 697 MET cc_start: 0.2268 (tmm) cc_final: 0.0968 (mpp) REVERT: A 886 MET cc_start: 0.2918 (tmm) cc_final: 0.2590 (tmt) REVERT: A 1330 LEU cc_start: -0.0171 (OUTLIER) cc_final: -0.0435 (mp) REVERT: A 1557 MET cc_start: -0.0523 (mmm) cc_final: -0.0846 (ttt) REVERT: A 1677 ILE cc_start: 0.6336 (pt) cc_final: 0.5938 (tt) REVERT: A 1713 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6626 (tmm160) REVERT: A 1840 GLN cc_start: 0.6484 (tt0) cc_final: 0.5938 (tt0) REVERT: A 1885 VAL cc_start: 0.3446 (m) cc_final: 0.3227 (m) REVERT: A 1989 GLU cc_start: 0.4360 (tp30) cc_final: 0.3346 (tp30) REVERT: A 2047 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7229 (mtt180) REVERT: A 2204 ASP cc_start: 0.5574 (t0) cc_final: 0.5236 (m-30) REVERT: B 1144 VAL cc_start: 0.5027 (t) cc_final: 0.4717 (t) REVERT: B 1147 MET cc_start: 0.5267 (mtt) cc_final: 0.4959 (ptt) REVERT: B 1402 HIS cc_start: 0.5494 (m-70) cc_final: 0.5167 (m-70) REVERT: B 1483 MET cc_start: 0.3275 (ttm) cc_final: 0.2803 (mmt) REVERT: B 1582 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6065 (tt) REVERT: B 1640 ASP cc_start: 0.5620 (p0) cc_final: 0.5158 (p0) REVERT: B 1688 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6901 (pp) REVERT: B 1731 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6873 (ptm160) REVERT: B 1750 TYR cc_start: 0.6227 (p90) cc_final: 0.5963 (p90) REVERT: B 1962 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: B 2000 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6546 (t0) REVERT: B 2138 ARG cc_start: 0.7589 (tpt90) cc_final: 0.7158 (tpm-80) REVERT: B 2277 GLN cc_start: 0.6344 (mm-40) cc_final: 0.5334 (pp30) REVERT: B 2321 HIS cc_start: 0.5390 (t70) cc_final: 0.4507 (t-90) REVERT: B 2322 MET cc_start: 0.5969 (mtm) cc_final: 0.5625 (mtm) REVERT: C 727 MET cc_start: 0.2712 (ttp) cc_final: 0.1959 (pmm) REVERT: C 886 MET cc_start: 0.4500 (tmm) cc_final: 0.4093 (mmp) REVERT: C 903 MET cc_start: 0.3406 (mtp) cc_final: 0.2340 (mmp) REVERT: C 912 PRO cc_start: 0.2901 (Cg_exo) cc_final: 0.2699 (Cg_endo) REVERT: C 939 GLN cc_start: 0.4564 (tp40) cc_final: 0.4233 (pm20) REVERT: C 959 GLU cc_start: 0.4365 (mp0) cc_final: 0.3961 (pt0) REVERT: C 1063 LEU cc_start: 0.4680 (mt) cc_final: 0.4414 (mp) REVERT: C 1153 TYR cc_start: 0.5571 (t80) cc_final: 0.5162 (t80) REVERT: C 1440 GLU cc_start: 0.4767 (mp0) cc_final: 0.4159 (mt-10) REVERT: C 1731 ARG cc_start: 0.2394 (OUTLIER) cc_final: 0.1240 (tmt170) REVERT: C 1795 GLU cc_start: 0.1713 (pm20) cc_final: 0.1293 (tm-30) outliers start: 74 outliers final: 16 residues processed: 828 average time/residue: 0.7861 time to fit residues: 785.1693 Evaluate side-chains 421 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 397 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1726 LEU Chi-restraints excluded: chain A residue 2040 LEU Chi-restraints excluded: chain A residue 2047 ARG Chi-restraints excluded: chain A residue 2127 LYS Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 1110 MET Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1581 ASP Chi-restraints excluded: chain B residue 1582 LEU Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1731 ARG Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 2000 ASP Chi-restraints excluded: chain B residue 2011 ILE Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2249 ARG Chi-restraints excluded: chain D residue 2040 LEU Chi-restraints excluded: chain C residue 1394 ILE Chi-restraints excluded: chain C residue 1581 ASP Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 2101 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 0.0060 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1061 ASN A1188 HIS A1534 ASN A1555 GLN A1682 ASN A1946 GLN A1965 GLN A2076 GLN A2146 HIS ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 HIS B1113 HIS ** B1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1384 ASN B1388 ASN B1882 HIS B1946 GLN B1965 GLN B2197 GLN B2291 ASN D1882 HIS D2059 GLN D2236 ASN C 924 GLN C 928 ASN C 993 GLN C1061 ASN C1089 HIS ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1287 HIS C1555 GLN C1694 GLN ** C1840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2028 GLN C2059 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.288381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.263704 restraints weight = 71116.682| |-----------------------------------------------------------------------------| r_work (start): 0.4935 rms_B_bonded: 2.52 r_work: 0.4646 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.4547 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40398 Z= 0.197 Angle : 0.689 9.769 54727 Z= 0.361 Chirality : 0.047 0.248 6098 Planarity : 0.006 0.060 7043 Dihedral : 7.552 58.531 5598 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.06 % Allowed : 11.40 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.11), residues: 4863 helix: 0.58 (0.11), residues: 2081 sheet: 0.31 (0.16), residues: 900 loop : -1.68 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1779 TYR 0.025 0.002 TYR C 994 PHE 0.029 0.002 PHE C2063 TRP 0.029 0.003 TRP A1936 HIS 0.011 0.001 HIS A2190 Details of bonding type rmsd covalent geometry : bond 0.00449 (40398) covalent geometry : angle 0.68857 (54727) hydrogen bonds : bond 0.04863 ( 1918) hydrogen bonds : angle 5.23599 ( 5532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 452 time to evaluate : 1.538 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: symmetry clash REVERT: A 886 MET cc_start: 0.2690 (tmm) cc_final: 0.2121 (ttm) REVERT: A 903 MET cc_start: 0.0601 (OUTLIER) cc_final: 0.0385 (tmt) REVERT: A 1021 MET cc_start: 0.2787 (mmp) cc_final: 0.1946 (mtm) REVERT: A 1110 MET cc_start: 0.1445 (mpt) cc_final: 0.1047 (pmm) REVERT: A 1307 MET cc_start: 0.1855 (ptm) cc_final: 0.0970 (mtp) REVERT: A 1483 MET cc_start: -0.2046 (ptp) cc_final: -0.2830 (tpp) REVERT: A 1557 MET cc_start: -0.0816 (mmm) cc_final: -0.1177 (ttt) REVERT: A 1582 LEU cc_start: 0.3398 (OUTLIER) cc_final: 0.3141 (tm) REVERT: B 857 LEU cc_start: 0.7277 (tt) cc_final: 0.6931 (tp) REVERT: B 963 MET cc_start: 0.3692 (mmm) cc_final: 0.3457 (mtt) REVERT: B 1080 ARG cc_start: 0.5384 (tpt170) cc_final: 0.5175 (tpp-160) REVERT: B 1401 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6477 (ppp) REVERT: B 1483 MET cc_start: 0.3690 (ttm) cc_final: 0.3342 (mmt) REVERT: B 1493 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6743 (ttm-80) REVERT: B 2035 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7494 (mtm180) REVERT: B 2190 HIS cc_start: 0.6845 (OUTLIER) cc_final: 0.5552 (p90) REVERT: B 2241 ASP cc_start: 0.6245 (m-30) cc_final: 0.5884 (m-30) REVERT: B 2258 THR cc_start: 0.6299 (OUTLIER) cc_final: 0.5937 (m) REVERT: D 1994 GLU cc_start: 0.2627 (OUTLIER) cc_final: 0.1924 (pt0) REVERT: D 2011 ILE cc_start: 0.1249 (OUTLIER) cc_final: 0.0201 (tt) REVERT: D 2053 MET cc_start: -0.0751 (mtp) cc_final: -0.1561 (tmt) REVERT: D 2056 MET cc_start: 0.2365 (mmm) cc_final: 0.1964 (mmp) REVERT: D 2105 MET cc_start: 0.2903 (tpt) cc_final: 0.2660 (tpt) REVERT: D 2107 MET cc_start: 0.0645 (tpt) cc_final: -0.1495 (ttm) REVERT: D 2276 LYS cc_start: 0.3730 (mmpt) cc_final: 0.2930 (tmtt) REVERT: C 629 MET cc_start: 0.2975 (mtp) cc_final: 0.2768 (mtp) REVERT: C 641 ASP cc_start: 0.3794 (t70) cc_final: 0.3512 (m-30) REVERT: C 747 LYS cc_start: 0.2991 (tttt) cc_final: 0.2570 (tptm) REVERT: C 903 MET cc_start: 0.3441 (mtp) cc_final: 0.3010 (mmp) REVERT: C 968 ILE cc_start: 0.1398 (mm) cc_final: 0.0764 (mm) REVERT: C 995 LEU cc_start: 0.3474 (OUTLIER) cc_final: 0.3141 (pp) REVERT: C 1401 MET cc_start: 0.2111 (mpp) cc_final: 0.1819 (mpp) REVERT: C 1418 ASP cc_start: 0.3781 (OUTLIER) cc_final: 0.3048 (m-30) REVERT: C 1493 ARG cc_start: 0.4853 (tpt90) cc_final: 0.3911 (ppt-90) REVERT: C 1731 ARG cc_start: 0.3067 (OUTLIER) cc_final: 0.1864 (tmt-80) REVERT: C 1795 GLU cc_start: 0.1873 (pm20) cc_final: 0.0776 (tm-30) REVERT: C 1864 THR cc_start: 0.3557 (OUTLIER) cc_final: 0.3283 (t) REVERT: C 1868 GLN cc_start: 0.3436 (mm110) cc_final: 0.2939 (tp40) REVERT: C 2105 MET cc_start: 0.0236 (tpt) cc_final: -0.1182 (tmm) outliers start: 133 outliers final: 40 residues processed: 542 average time/residue: 0.7585 time to fit residues: 500.5624 Evaluate side-chains 395 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1646 VAL Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1746 LYS Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2011 ILE Chi-restraints excluded: chain A residue 2126 ILE Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 903 MET Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1401 MET Chi-restraints excluded: chain B residue 1493 ARG Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2258 THR Chi-restraints excluded: chain B residue 2320 ILE Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1802 MET Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2292 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1421 PHE Chi-restraints excluded: chain C residue 1447 GLU Chi-restraints excluded: chain C residue 1678 ILE Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1864 THR Chi-restraints excluded: chain C residue 1881 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 428 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 409 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 358 optimal weight: 30.0000 chunk 140 optimal weight: 0.5980 chunk 480 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 ASN A1168 HIS A1462 ASN A1647 HIS A1914 ASN ** A1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2076 GLN A2267 ASN A2285 HIS A2291 ASN ** B 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1097 HIS ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1384 ASN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 HIS D1878 ASN ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 993 GLN C1031 HIS C1140 HIS ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1188 HIS C1840 GLN C1843 ASN C2028 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.285060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.260180 restraints weight = 68193.086| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 2.50 r_work: 0.4631 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.4587 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.137 40398 Z= 0.418 Angle : 0.941 14.880 54727 Z= 0.497 Chirality : 0.058 0.327 6098 Planarity : 0.008 0.110 7043 Dihedral : 7.882 89.355 5553 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 5.01 % Allowed : 12.55 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.11), residues: 4863 helix: -0.03 (0.11), residues: 2129 sheet: 0.22 (0.16), residues: 891 loop : -2.08 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A2212 TYR 0.075 0.004 TYR A1932 PHE 0.038 0.004 PHE A1666 TRP 0.058 0.005 TRP A2018 HIS 0.022 0.003 HIS A2190 Details of bonding type rmsd covalent geometry : bond 0.00969 (40398) covalent geometry : angle 0.94070 (54727) hydrogen bonds : bond 0.06447 ( 1918) hydrogen bonds : angle 5.66526 ( 5532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 407 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 MET cc_start: 0.0876 (mmm) cc_final: -0.0973 (pmt) REVERT: A 864 MET cc_start: 0.2385 (tmt) cc_final: 0.1976 (tpp) REVERT: A 886 MET cc_start: 0.2406 (tmm) cc_final: 0.2063 (ttm) REVERT: A 922 MET cc_start: 0.0267 (tmm) cc_final: -0.1404 (pmt) REVERT: A 983 MET cc_start: 0.2743 (tmm) cc_final: 0.2372 (tmm) REVERT: A 1021 MET cc_start: 0.3490 (mmp) cc_final: 0.1897 (mtm) REVERT: A 1483 MET cc_start: -0.1766 (OUTLIER) cc_final: -0.2724 (tpp) REVERT: A 1557 MET cc_start: -0.0880 (mmm) cc_final: -0.1632 (ttt) REVERT: A 1745 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: A 1937 MET cc_start: 0.7413 (ptt) cc_final: 0.7203 (ptt) REVERT: A 1964 MET cc_start: 0.7397 (mtm) cc_final: 0.6924 (mtp) REVERT: A 1970 THR cc_start: 0.6823 (OUTLIER) cc_final: 0.6265 (p) REVERT: A 2069 ASP cc_start: 0.7441 (m-30) cc_final: 0.7011 (m-30) REVERT: A 2325 HIS cc_start: 0.5317 (p-80) cc_final: 0.5116 (p-80) REVERT: B 684 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6059 (mtmm) REVERT: B 697 MET cc_start: 0.3162 (tpt) cc_final: 0.2927 (tpt) REVERT: B 1493 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6930 (ttm-80) REVERT: B 1688 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7485 (pp) REVERT: B 1962 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: B 2035 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7759 (mtm180) REVERT: B 2103 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8179 (tpt-90) REVERT: B 2162 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5255 (mmtm) REVERT: B 2190 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.6874 (m90) REVERT: D 1994 GLU cc_start: 0.3051 (OUTLIER) cc_final: 0.2297 (pt0) REVERT: D 2003 ASN cc_start: 0.2929 (OUTLIER) cc_final: 0.0810 (m-40) REVERT: D 2056 MET cc_start: 0.2673 (mmm) cc_final: 0.2204 (mmp) REVERT: D 2105 MET cc_start: 0.3378 (tpt) cc_final: 0.2944 (tpt) REVERT: D 2107 MET cc_start: 0.1065 (tpt) cc_final: -0.1167 (ttm) REVERT: D 2231 LYS cc_start: 0.3293 (OUTLIER) cc_final: 0.2521 (mtmm) REVERT: D 2276 LYS cc_start: 0.4295 (mmpt) cc_final: 0.3455 (tmtt) REVERT: C 747 LYS cc_start: 0.3706 (tttt) cc_final: 0.3107 (tptm) REVERT: C 959 GLU cc_start: 0.4155 (OUTLIER) cc_final: 0.3675 (pp20) REVERT: C 988 MET cc_start: 0.0876 (ptt) cc_final: 0.0528 (mtt) REVERT: C 995 LEU cc_start: 0.3252 (OUTLIER) cc_final: 0.2653 (tp) REVERT: C 1233 MET cc_start: 0.4763 (ptp) cc_final: 0.4537 (ptp) REVERT: C 1364 PHE cc_start: 0.1888 (t80) cc_final: 0.0918 (t80) REVERT: C 1386 MET cc_start: 0.2998 (mmm) cc_final: 0.2395 (ppp) REVERT: C 1731 ARG cc_start: 0.3208 (OUTLIER) cc_final: 0.1655 (tmt170) REVERT: C 1795 GLU cc_start: 0.2269 (pm20) cc_final: 0.1188 (tp30) REVERT: C 1868 GLN cc_start: 0.3490 (mm110) cc_final: 0.3111 (mp10) outliers start: 218 outliers final: 78 residues processed: 562 average time/residue: 0.7420 time to fit residues: 509.0124 Evaluate side-chains 407 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 312 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1784 ASP Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1860 ARG Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1943 HIS Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2185 GLN Chi-restraints excluded: chain A residue 2211 SER Chi-restraints excluded: chain A residue 2213 THR Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain B residue 1145 VAL Chi-restraints excluded: chain B residue 1183 MET Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1319 LEU Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1493 ARG Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1530 LEU Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1928 THR Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 1961 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2103 ARG Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2114 ARG Chi-restraints excluded: chain B residue 2162 LYS Chi-restraints excluded: chain B residue 2176 ILE Chi-restraints excluded: chain B residue 2182 VAL Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2191 ASP Chi-restraints excluded: chain B residue 2211 SER Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2226 ASP Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1802 MET Chi-restraints excluded: chain D residue 1830 TYR Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2099 SER Chi-restraints excluded: chain D residue 2231 LYS Chi-restraints excluded: chain D residue 2248 LEU Chi-restraints excluded: chain D residue 2292 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 974 ARG Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1447 GLU Chi-restraints excluded: chain C residue 1553 THR Chi-restraints excluded: chain C residue 1572 LEU Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1843 ASN Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 250 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 286 optimal weight: 0.4980 chunk 264 optimal weight: 0.7980 chunk 408 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 472 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 ASN A1569 HIS A2076 GLN A2104 HIS ** A2185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2243 GLN B 664 HIS B 688 GLN B1026 ASN B1074 ASN B1113 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1384 ASN B1443 GLN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1555 GLN ** B1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2190 HIS ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 GLN C 993 GLN C1167 GLN C1565 GLN C1682 ASN C1868 GLN ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.284048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.258153 restraints weight = 70107.719| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 2.55 r_work: 0.4489 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40398 Z= 0.136 Angle : 0.640 12.419 54727 Z= 0.328 Chirality : 0.045 0.185 6098 Planarity : 0.005 0.076 7043 Dihedral : 7.125 86.074 5553 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.29 % Allowed : 15.61 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.12), residues: 4863 helix: 0.68 (0.11), residues: 2116 sheet: 0.40 (0.17), residues: 902 loop : -1.76 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2331 TYR 0.026 0.002 TYR A2179 PHE 0.035 0.002 PHE D2063 TRP 0.033 0.002 TRP C1967 HIS 0.007 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00291 (40398) covalent geometry : angle 0.64010 (54727) hydrogen bonds : bond 0.04135 ( 1918) hydrogen bonds : angle 5.02381 ( 5532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 365 time to evaluate : 1.546 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 629 MET cc_start: 0.0612 (OUTLIER) cc_final: -0.0862 (pmt) REVERT: A 864 MET cc_start: 0.1780 (tmt) cc_final: 0.1298 (tpp) REVERT: A 886 MET cc_start: 0.2759 (tmm) cc_final: 0.2208 (ttm) REVERT: A 922 MET cc_start: 0.0713 (tmm) cc_final: -0.1061 (pmm) REVERT: A 983 MET cc_start: 0.3290 (tmm) cc_final: 0.2888 (tmm) REVERT: A 1009 CYS cc_start: 0.1814 (OUTLIER) cc_final: 0.1441 (p) REVERT: A 1021 MET cc_start: 0.3508 (mmp) cc_final: 0.1963 (mtm) REVERT: A 1483 MET cc_start: -0.2287 (ptp) cc_final: -0.3067 (tpp) REVERT: A 1557 MET cc_start: -0.0969 (mmm) cc_final: -0.1537 (ttt) REVERT: A 1745 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: A 1964 MET cc_start: 0.7231 (mtm) cc_final: 0.6791 (mtp) REVERT: B 697 MET cc_start: 0.3508 (tpt) cc_final: 0.3207 (tpt) REVERT: B 1066 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7462 (tt) REVERT: B 1140 HIS cc_start: 0.3447 (OUTLIER) cc_final: 0.2293 (t-90) REVERT: B 1385 ARG cc_start: 0.6678 (tpp-160) cc_final: 0.6281 (tpp-160) REVERT: B 1457 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6341 (tt) REVERT: B 1483 MET cc_start: 0.4009 (ttm) cc_final: 0.2699 (mmt) REVERT: B 1493 ARG cc_start: 0.7173 (ttp-170) cc_final: 0.6824 (ttm-80) REVERT: B 1688 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6703 (pp) REVERT: B 1962 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: B 2040 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7833 (tt) REVERT: D 1994 GLU cc_start: 0.2541 (OUTLIER) cc_final: 0.1682 (pp20) REVERT: D 2003 ASN cc_start: 0.2501 (OUTLIER) cc_final: 0.0656 (m-40) REVERT: D 2053 MET cc_start: -0.0038 (OUTLIER) cc_final: -0.2578 (tmt) REVERT: D 2056 MET cc_start: 0.2633 (mmm) cc_final: 0.1845 (mmp) REVERT: D 2105 MET cc_start: 0.2857 (tpt) cc_final: 0.2080 (tpt) REVERT: D 2107 MET cc_start: 0.0895 (tpt) cc_final: -0.1372 (ttm) REVERT: C 632 VAL cc_start: 0.2368 (m) cc_final: 0.2147 (m) REVERT: C 912 PRO cc_start: 0.2937 (Cg_exo) cc_final: 0.2597 (Cg_endo) REVERT: C 995 LEU cc_start: 0.3360 (OUTLIER) cc_final: 0.2852 (tp) REVERT: C 1364 PHE cc_start: 0.2424 (t80) cc_final: 0.1094 (t80) REVERT: C 1386 MET cc_start: 0.3242 (mmm) cc_final: 0.2258 (ppp) REVERT: C 1401 MET cc_start: 0.1975 (mpp) cc_final: 0.0937 (pmm) REVERT: C 1418 ASP cc_start: 0.3276 (OUTLIER) cc_final: 0.2553 (t0) REVERT: C 1449 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.4992 (tp) REVERT: C 1493 ARG cc_start: 0.4395 (tpt90) cc_final: 0.4081 (ppt-90) REVERT: C 1731 ARG cc_start: 0.2519 (OUTLIER) cc_final: 0.1113 (tmt170) REVERT: C 1795 GLU cc_start: 0.1564 (pm20) cc_final: 0.0458 (tp30) REVERT: C 1814 ILE cc_start: 0.1144 (OUTLIER) cc_final: 0.0527 (mm) REVERT: C 1902 MET cc_start: 0.0343 (OUTLIER) cc_final: 0.0073 (ptp) outliers start: 143 outliers final: 50 residues processed: 471 average time/residue: 0.6773 time to fit residues: 394.5995 Evaluate side-chains 380 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1848 LEU Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 2168 LEU Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 664 HIS Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1140 HIS Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1388 ASN Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1929 LYS Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2053 MET Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2244 ILE Chi-restraints excluded: chain D residue 2248 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1449 LEU Chi-restraints excluded: chain C residue 1452 GLU Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1814 ILE Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1864 THR Chi-restraints excluded: chain C residue 1902 MET Chi-restraints excluded: chain C residue 2053 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 212 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 324 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 289 optimal weight: 0.5980 chunk 97 optimal weight: 0.0070 chunk 114 optimal weight: 0.0030 chunk 453 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2076 GLN ** A2185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 HIS ** A2267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2325 HIS B 664 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 HIS B2190 HIS C 939 GLN ** C 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.283954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.258438 restraints weight = 69461.599| |-----------------------------------------------------------------------------| r_work (start): 0.4890 rms_B_bonded: 2.52 r_work: 0.4554 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4445 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40398 Z= 0.122 Angle : 0.606 12.539 54727 Z= 0.310 Chirality : 0.043 0.169 6098 Planarity : 0.004 0.067 7043 Dihedral : 6.820 85.201 5553 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.90 % Allowed : 16.59 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.12), residues: 4863 helix: 0.91 (0.11), residues: 2121 sheet: 0.62 (0.17), residues: 874 loop : -1.61 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG B1760 TYR 0.021 0.001 TYR B 994 PHE 0.040 0.002 PHE B1011 TRP 0.023 0.002 TRP C1662 HIS 0.013 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00264 (40398) covalent geometry : angle 0.60562 (54727) hydrogen bonds : bond 0.03877 ( 1918) hydrogen bonds : angle 4.85001 ( 5532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 341 time to evaluate : 1.330 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 864 MET cc_start: 0.2093 (tmt) cc_final: 0.1394 (tpp) REVERT: A 886 MET cc_start: 0.2747 (tmm) cc_final: 0.2268 (ttm) REVERT: A 922 MET cc_start: 0.0646 (tmm) cc_final: -0.1061 (pmm) REVERT: A 1009 CYS cc_start: 0.1959 (OUTLIER) cc_final: 0.1243 (p) REVERT: A 1021 MET cc_start: 0.3509 (mmp) cc_final: 0.1994 (mtm) REVERT: A 1483 MET cc_start: -0.2328 (ptp) cc_final: -0.3045 (tpp) REVERT: A 1557 MET cc_start: -0.1201 (mmm) cc_final: -0.1677 (ttt) REVERT: A 1745 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: A 1889 PHE cc_start: 0.5529 (OUTLIER) cc_final: 0.4715 (t80) REVERT: A 1964 MET cc_start: 0.7265 (mtm) cc_final: 0.6918 (mtp) REVERT: A 2137 MET cc_start: 0.3342 (OUTLIER) cc_final: 0.2924 (ttp) REVERT: A 2168 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.5025 (mm) REVERT: B 697 MET cc_start: 0.3501 (tpt) cc_final: 0.0706 (mtm) REVERT: B 1028 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6852 (pp) REVERT: B 1066 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 1233 MET cc_start: 0.5336 (ppp) cc_final: 0.4697 (tmm) REVERT: B 1319 LEU cc_start: 0.6121 (tm) cc_final: 0.5372 (pt) REVERT: B 1385 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6314 (tpp-160) REVERT: B 1457 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6184 (tt) REVERT: B 1483 MET cc_start: 0.3766 (ttm) cc_final: 0.2651 (mmt) REVERT: B 1493 ARG cc_start: 0.7158 (ttp-170) cc_final: 0.6840 (ttm-80) REVERT: B 1688 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6884 (pp) REVERT: B 1962 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: B 2040 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7767 (tt) REVERT: B 2190 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6585 (p-80) REVERT: B 2213 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6540 (m) REVERT: D 1994 GLU cc_start: 0.2712 (OUTLIER) cc_final: 0.1850 (pp20) REVERT: D 2003 ASN cc_start: 0.2602 (OUTLIER) cc_final: 0.0639 (m-40) REVERT: D 2053 MET cc_start: 0.0493 (OUTLIER) cc_final: -0.1850 (tmt) REVERT: D 2056 MET cc_start: 0.2567 (mmm) cc_final: 0.1857 (mmp) REVERT: D 2105 MET cc_start: 0.3063 (tpt) cc_final: 0.2535 (tpt) REVERT: D 2107 MET cc_start: 0.0753 (tpt) cc_final: -0.1399 (ttm) REVERT: D 2231 LYS cc_start: 0.3163 (OUTLIER) cc_final: 0.2660 (mtmm) REVERT: C 887 LYS cc_start: 0.5464 (mmpt) cc_final: 0.5149 (ttmt) REVERT: C 912 PRO cc_start: 0.3436 (Cg_exo) cc_final: 0.3182 (Cg_endo) REVERT: C 963 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3617 (tmt) REVERT: C 995 LEU cc_start: 0.3404 (OUTLIER) cc_final: 0.2840 (tp) REVERT: C 1364 PHE cc_start: 0.2291 (t80) cc_final: 0.1141 (t80) REVERT: C 1369 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3288 (mt) REVERT: C 1386 MET cc_start: 0.3075 (mmm) cc_final: 0.2148 (ppp) REVERT: C 1401 MET cc_start: 0.1783 (mpp) cc_final: 0.0989 (pmm) REVERT: C 1404 TYR cc_start: 0.3431 (OUTLIER) cc_final: 0.2695 (m-80) REVERT: C 1418 ASP cc_start: 0.2967 (OUTLIER) cc_final: 0.2266 (t0) REVERT: C 1497 MET cc_start: 0.2304 (mtp) cc_final: 0.1590 (tpt) REVERT: C 1557 MET cc_start: 0.2185 (tpt) cc_final: 0.1006 (mpp) REVERT: C 1731 ARG cc_start: 0.2761 (OUTLIER) cc_final: 0.1531 (tmt170) REVERT: C 1795 GLU cc_start: 0.1795 (pm20) cc_final: 0.0592 (tp30) REVERT: C 1814 ILE cc_start: 0.0975 (OUTLIER) cc_final: 0.0672 (mm) REVERT: C 1902 MET cc_start: 0.0553 (OUTLIER) cc_final: 0.0255 (ptp) outliers start: 126 outliers final: 50 residues processed: 436 average time/residue: 0.6371 time to fit residues: 342.8483 Evaluate side-chains 391 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 315 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1889 PHE Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2168 LEU Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1028 ILE Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1183 MET Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1385 ARG Chi-restraints excluded: chain B residue 1388 ASN Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2053 MET Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2231 LYS Chi-restraints excluded: chain D residue 2244 ILE Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1093 TYR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1404 TYR Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1814 ILE Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1902 MET Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 244 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 464 optimal weight: 6.9990 chunk 400 optimal weight: 0.3980 chunk 318 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 309 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1943 HIS A2190 HIS A2325 HIS B1005 HIS B1074 ASN ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2190 HIS C 948 HIS C 982 HIS ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1868 GLN ** C1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.282427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.256055 restraints weight = 67943.421| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 2.52 r_work: 0.4593 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.4522 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 40398 Z= 0.260 Angle : 0.728 11.090 54727 Z= 0.376 Chirality : 0.048 0.263 6098 Planarity : 0.006 0.103 7043 Dihedral : 7.089 85.227 5551 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 3.42 % Allowed : 16.75 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.12), residues: 4863 helix: 0.62 (0.11), residues: 2137 sheet: 0.40 (0.17), residues: 889 loop : -1.74 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 992 TYR 0.040 0.002 TYR B 994 PHE 0.045 0.003 PHE B1011 TRP 0.035 0.003 TRP A2018 HIS 0.028 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00605 (40398) covalent geometry : angle 0.72797 (54727) hydrogen bonds : bond 0.04889 ( 1918) hydrogen bonds : angle 5.09396 ( 5532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 334 time to evaluate : 1.054 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 629 MET cc_start: 0.0856 (mmm) cc_final: -0.0871 (pmt) REVERT: A 864 MET cc_start: 0.2426 (tmt) cc_final: 0.1478 (ttm) REVERT: A 886 MET cc_start: 0.3095 (tmm) cc_final: 0.2652 (ttm) REVERT: A 922 MET cc_start: 0.0499 (tmm) cc_final: -0.1168 (pmm) REVERT: A 983 MET cc_start: 0.2727 (tmm) cc_final: 0.2198 (tmm) REVERT: A 1009 CYS cc_start: 0.2010 (OUTLIER) cc_final: 0.1116 (p) REVERT: A 1021 MET cc_start: 0.4085 (mmp) cc_final: 0.2132 (mtm) REVERT: A 1483 MET cc_start: -0.1893 (ptp) cc_final: -0.2955 (tpp) REVERT: A 1745 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: A 1880 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8130 (t) REVERT: A 1964 MET cc_start: 0.7352 (mtm) cc_final: 0.6964 (mtp) REVERT: A 1970 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6275 (p) REVERT: A 2226 ASP cc_start: 0.6111 (m-30) cc_final: 0.5897 (m-30) REVERT: B 697 MET cc_start: 0.3830 (tpt) cc_final: 0.0980 (mtm) REVERT: B 1005 HIS cc_start: 0.5126 (OUTLIER) cc_final: 0.4829 (t-170) REVERT: B 1066 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7368 (tt) REVERT: B 1385 ARG cc_start: 0.6531 (tpp-160) cc_final: 0.6317 (tpp-160) REVERT: B 1457 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6160 (tt) REVERT: B 1483 MET cc_start: 0.4303 (ttm) cc_final: 0.3114 (mmt) REVERT: B 1493 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7008 (ttm-80) REVERT: B 1688 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7026 (pp) REVERT: B 1962 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: B 2035 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7602 (mtm180) REVERT: B 2103 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7111 (tpt-90) REVERT: B 2190 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.6875 (p-80) REVERT: B 2213 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6605 (m) REVERT: B 2247 MET cc_start: 0.6989 (ttm) cc_final: 0.6728 (ttt) REVERT: D 1994 GLU cc_start: 0.2810 (OUTLIER) cc_final: 0.2023 (pp20) REVERT: D 2003 ASN cc_start: 0.2946 (OUTLIER) cc_final: 0.0757 (m-40) REVERT: D 2053 MET cc_start: -0.0365 (OUTLIER) cc_final: -0.2081 (tmt) REVERT: D 2056 MET cc_start: 0.2753 (mmm) cc_final: 0.2117 (mmp) REVERT: D 2107 MET cc_start: 0.0885 (tpt) cc_final: -0.1271 (ttm) REVERT: C 728 LYS cc_start: 0.3076 (mppt) cc_final: 0.2114 (tptt) REVERT: C 887 LYS cc_start: 0.5452 (mmpt) cc_final: 0.5082 (ttmt) REVERT: C 912 PRO cc_start: 0.3437 (Cg_exo) cc_final: 0.3183 (Cg_endo) REVERT: C 959 GLU cc_start: 0.3753 (OUTLIER) cc_final: 0.3536 (pt0) REVERT: C 963 MET cc_start: 0.4060 (OUTLIER) cc_final: 0.3626 (tmt) REVERT: C 995 LEU cc_start: 0.3483 (OUTLIER) cc_final: 0.2782 (tp) REVERT: C 1236 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.4593 (tpp) REVERT: C 1386 MET cc_start: 0.3271 (mmm) cc_final: 0.2314 (ppp) REVERT: C 1401 MET cc_start: 0.2083 (mpp) cc_final: 0.1054 (pmm) REVERT: C 1404 TYR cc_start: 0.3148 (OUTLIER) cc_final: 0.2513 (m-80) REVERT: C 1418 ASP cc_start: 0.3271 (OUTLIER) cc_final: 0.2380 (t0) REVERT: C 1571 MET cc_start: 0.1574 (ptp) cc_final: 0.1311 (ptp) REVERT: C 1631 MET cc_start: -0.0408 (tpt) cc_final: -0.4225 (mtm) REVERT: C 1731 ARG cc_start: 0.3147 (OUTLIER) cc_final: 0.1695 (tmt170) REVERT: C 1795 GLU cc_start: 0.2506 (pm20) cc_final: 0.1136 (tp30) REVERT: C 1814 ILE cc_start: 0.1228 (OUTLIER) cc_final: 0.0805 (mm) outliers start: 149 outliers final: 72 residues processed: 444 average time/residue: 0.5938 time to fit residues: 326.1590 Evaluate side-chains 400 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 303 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1610 ILE Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1860 ARG Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1941 ARG Chi-restraints excluded: chain A residue 1943 HIS Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2168 LEU Chi-restraints excluded: chain A residue 2245 GLN Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1183 MET Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1384 ASN Chi-restraints excluded: chain B residue 1388 ASN Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1493 ARG Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1703 SER Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1761 VAL Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1928 THR Chi-restraints excluded: chain B residue 1929 LYS Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2088 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2103 ARG Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2182 VAL Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2226 ASP Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1802 MET Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2053 MET Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1093 TYR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1404 TYR Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1814 ILE Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 2030 ILE Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 64 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 333 optimal weight: 0.0030 chunk 43 optimal weight: 8.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 HIS A2076 GLN A2190 HIS A2325 HIS B1005 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2190 HIS C 982 HIS ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1868 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.286450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.260402 restraints weight = 68200.884| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 2.50 r_work: 0.4523 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40398 Z= 0.146 Angle : 0.638 11.886 54727 Z= 0.326 Chirality : 0.044 0.323 6098 Planarity : 0.005 0.068 7043 Dihedral : 6.838 86.787 5551 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.22 % Allowed : 17.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.12), residues: 4863 helix: 0.85 (0.11), residues: 2128 sheet: 0.56 (0.17), residues: 877 loop : -1.64 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2138 TYR 0.036 0.001 TYR B 994 PHE 0.057 0.002 PHE B1011 TRP 0.029 0.002 TRP C1662 HIS 0.011 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00328 (40398) covalent geometry : angle 0.63799 (54727) hydrogen bonds : bond 0.04047 ( 1918) hydrogen bonds : angle 4.90056 ( 5532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 337 time to evaluate : 0.972 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 864 MET cc_start: 0.2166 (tmt) cc_final: 0.1309 (ttm) REVERT: A 886 MET cc_start: 0.2927 (tmm) cc_final: 0.2411 (ttm) REVERT: A 922 MET cc_start: 0.0491 (tmm) cc_final: -0.1138 (pmm) REVERT: A 1009 CYS cc_start: 0.1980 (OUTLIER) cc_final: 0.1118 (p) REVERT: A 1021 MET cc_start: 0.4042 (OUTLIER) cc_final: 0.2079 (mtm) REVERT: A 1483 MET cc_start: -0.1986 (ptp) cc_final: -0.3039 (tpp) REVERT: A 1745 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: A 1880 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 1889 PHE cc_start: 0.5353 (m-80) cc_final: 0.4737 (t80) REVERT: A 1964 MET cc_start: 0.7169 (mtm) cc_final: 0.6818 (mtp) REVERT: A 1970 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6202 (p) REVERT: A 2137 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3334 (ttp) REVERT: A 2226 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.5520 (t70) REVERT: B 697 MET cc_start: 0.3745 (tpt) cc_final: 0.0691 (mtm) REVERT: B 1066 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7521 (tt) REVERT: B 1385 ARG cc_start: 0.6541 (tpp-160) cc_final: 0.6232 (tpp-160) REVERT: B 1457 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6259 (tt) REVERT: B 1483 MET cc_start: 0.3921 (ttm) cc_final: 0.2774 (mmt) REVERT: B 1493 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6999 (ttm-80) REVERT: B 1688 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6711 (pp) REVERT: B 1962 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: B 2035 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7434 (mtm180) REVERT: B 2040 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7889 (tt) REVERT: B 2190 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6706 (p-80) REVERT: B 2199 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (mptp) REVERT: D 1817 ILE cc_start: 0.2267 (pp) cc_final: 0.2026 (mp) REVERT: D 1875 MET cc_start: -0.0199 (mmp) cc_final: -0.1737 (mmp) REVERT: D 1994 GLU cc_start: 0.2824 (OUTLIER) cc_final: 0.1891 (pp20) REVERT: D 2003 ASN cc_start: 0.2509 (OUTLIER) cc_final: 0.0495 (m-40) REVERT: D 2053 MET cc_start: -0.0100 (mtt) cc_final: -0.1194 (tmt) REVERT: D 2056 MET cc_start: 0.2543 (mmm) cc_final: 0.1974 (mmp) REVERT: D 2107 MET cc_start: 0.0602 (tpt) cc_final: -0.1464 (ttm) REVERT: D 2231 LYS cc_start: 0.3208 (OUTLIER) cc_final: 0.2623 (mtmm) REVERT: C 728 LYS cc_start: 0.3145 (mppt) cc_final: 0.2294 (tptt) REVERT: C 887 LYS cc_start: 0.5490 (mmpt) cc_final: 0.5248 (ttmt) REVERT: C 912 PRO cc_start: 0.3199 (Cg_exo) cc_final: 0.2991 (Cg_endo) REVERT: C 963 MET cc_start: 0.3836 (OUTLIER) cc_final: 0.3494 (tmt) REVERT: C 995 LEU cc_start: 0.3532 (OUTLIER) cc_final: 0.2842 (tp) REVERT: C 1046 ASP cc_start: 0.3251 (t0) cc_final: 0.2913 (t0) REVERT: C 1236 MET cc_start: 0.4734 (OUTLIER) cc_final: 0.4533 (tpp) REVERT: C 1364 PHE cc_start: 0.2500 (t80) cc_final: 0.1182 (t80) REVERT: C 1369 ILE cc_start: 0.4201 (OUTLIER) cc_final: 0.3201 (mt) REVERT: C 1386 MET cc_start: 0.3113 (mmm) cc_final: 0.2008 (ppp) REVERT: C 1401 MET cc_start: 0.2186 (mpp) cc_final: 0.1334 (pmm) REVERT: C 1404 TYR cc_start: 0.3614 (OUTLIER) cc_final: 0.2949 (m-80) REVERT: C 1418 ASP cc_start: 0.3059 (OUTLIER) cc_final: 0.2189 (t0) REVERT: C 1557 MET cc_start: 0.1891 (tpt) cc_final: 0.0829 (mpp) REVERT: C 1631 MET cc_start: -0.0865 (tpt) cc_final: -0.4473 (mtm) REVERT: C 1731 ARG cc_start: 0.2798 (OUTLIER) cc_final: 0.1686 (tmt-80) REVERT: C 1795 GLU cc_start: 0.2031 (pm20) cc_final: 0.0782 (tp30) REVERT: C 1814 ILE cc_start: 0.0987 (OUTLIER) cc_final: 0.0764 (mm) outliers start: 140 outliers final: 61 residues processed: 449 average time/residue: 0.5873 time to fit residues: 328.1708 Evaluate side-chains 399 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 312 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1880 VAL Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1926 VAL Chi-restraints excluded: chain A residue 1943 HIS Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2226 ASP Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 934 CYS Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1183 MET Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1388 ASN Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1703 SER Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2114 ARG Chi-restraints excluded: chain B residue 2128 PHE Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2191 ASP Chi-restraints excluded: chain B residue 2199 LYS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1802 MET Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2231 LYS Chi-restraints excluded: chain C residue 934 CYS Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1093 TYR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1404 TYR Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1814 ILE Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1864 THR Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 7.9990 chunk 427 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 373 optimal weight: 0.0670 chunk 423 optimal weight: 6.9990 chunk 387 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 323 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 HIS B1005 HIS B1443 GLN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1516 ASN B1765 ASN D1878 ASN C 982 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1167 GLN ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1181 GLN C1388 ASN C1868 GLN ** C1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.280306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.252193 restraints weight = 68341.016| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 2.61 r_work: 0.4503 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.130 40398 Z= 0.387 Angle : 0.890 17.328 54727 Z= 0.463 Chirality : 0.055 0.417 6098 Planarity : 0.007 0.114 7043 Dihedral : 7.526 79.663 5551 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 3.65 % Allowed : 17.88 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.12), residues: 4863 helix: 0.15 (0.11), residues: 2135 sheet: 0.31 (0.17), residues: 843 loop : -1.96 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1675 TYR 0.046 0.003 TYR B 994 PHE 0.052 0.003 PHE B1011 TRP 0.047 0.004 TRP A2018 HIS 0.033 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00900 (40398) covalent geometry : angle 0.88957 (54727) hydrogen bonds : bond 0.05915 ( 1918) hydrogen bonds : angle 5.52787 ( 5532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 334 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 MET cc_start: 0.2405 (tmt) cc_final: 0.1732 (ttm) REVERT: A 886 MET cc_start: 0.2979 (tmm) cc_final: 0.2469 (ttm) REVERT: A 922 MET cc_start: 0.0690 (tmm) cc_final: -0.1706 (pmm) REVERT: A 1009 CYS cc_start: 0.2437 (OUTLIER) cc_final: 0.1262 (p) REVERT: A 1021 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.2528 (mtm) REVERT: A 1745 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: A 1941 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5222 (ptm160) REVERT: A 1964 MET cc_start: 0.7285 (mtm) cc_final: 0.6803 (mtp) REVERT: A 1970 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6363 (p) REVERT: A 2168 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4499 (pp) REVERT: A 2212 ARG cc_start: 0.5878 (mtp-110) cc_final: 0.4954 (mmm160) REVERT: B 693 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.4381 (m-80) REVERT: B 697 MET cc_start: 0.3930 (tpt) cc_final: 0.0997 (mtm) REVERT: B 864 MET cc_start: 0.5722 (tpp) cc_final: 0.5461 (mmt) REVERT: B 903 MET cc_start: 0.4556 (mpp) cc_final: 0.2995 (mmt) REVERT: B 1005 HIS cc_start: 0.4687 (OUTLIER) cc_final: 0.4375 (t-170) REVERT: B 1066 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7567 (tt) REVERT: B 1385 ARG cc_start: 0.6642 (tpp-160) cc_final: 0.6342 (tpp-160) REVERT: B 1457 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6525 (tt) REVERT: B 1483 MET cc_start: 0.5099 (ttm) cc_final: 0.3241 (mmt) REVERT: B 1688 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7248 (pp) REVERT: B 2035 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7653 (mtm180) REVERT: B 2103 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7109 (tpt-90) REVERT: D 1994 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.1940 (pt0) REVERT: D 2003 ASN cc_start: 0.3027 (OUTLIER) cc_final: 0.0802 (m-40) REVERT: D 2011 ILE cc_start: 0.1420 (OUTLIER) cc_final: 0.0664 (mt) REVERT: D 2053 MET cc_start: 0.0289 (mtt) cc_final: -0.1215 (tmt) REVERT: D 2056 MET cc_start: 0.2306 (mmm) cc_final: 0.1889 (mmp) REVERT: D 2105 MET cc_start: 0.3554 (tpt) cc_final: 0.2932 (mmm) REVERT: D 2107 MET cc_start: 0.0992 (tpt) cc_final: -0.1232 (ttm) REVERT: C 727 MET cc_start: 0.3339 (mtp) cc_final: 0.2116 (tmt) REVERT: C 728 LYS cc_start: 0.3471 (mppt) cc_final: 0.2052 (tptt) REVERT: C 912 PRO cc_start: 0.3494 (Cg_exo) cc_final: 0.3186 (Cg_endo) REVERT: C 959 GLU cc_start: 0.3848 (OUTLIER) cc_final: 0.3496 (pt0) REVERT: C 963 MET cc_start: 0.4079 (OUTLIER) cc_final: 0.3584 (tmt) REVERT: C 983 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.2532 (tpt) REVERT: C 995 LEU cc_start: 0.3800 (OUTLIER) cc_final: 0.3453 (pp) REVERT: C 1386 MET cc_start: 0.3391 (mmm) cc_final: 0.2534 (ppp) REVERT: C 1401 MET cc_start: 0.2380 (mpp) cc_final: 0.1277 (pmm) REVERT: C 1404 TYR cc_start: 0.3554 (OUTLIER) cc_final: 0.2930 (m-80) REVERT: C 1418 ASP cc_start: 0.3447 (OUTLIER) cc_final: 0.2393 (t0) REVERT: C 1421 PHE cc_start: 0.3285 (m-10) cc_final: 0.2866 (m-10) REVERT: C 1489 GLU cc_start: 0.4134 (mm-30) cc_final: 0.3332 (tp30) REVERT: C 1616 MET cc_start: -0.0282 (mtt) cc_final: -0.0810 (mtm) REVERT: C 1731 ARG cc_start: 0.2966 (OUTLIER) cc_final: 0.1622 (ttt-90) REVERT: C 1788 LYS cc_start: 0.4532 (tppt) cc_final: 0.3636 (mmmt) REVERT: C 1795 GLU cc_start: 0.2383 (pm20) cc_final: 0.0948 (tp30) REVERT: C 1814 ILE cc_start: 0.1494 (OUTLIER) cc_final: 0.1015 (mm) REVERT: C 1816 THR cc_start: 0.1055 (OUTLIER) cc_final: 0.0718 (t) outliers start: 159 outliers final: 82 residues processed: 457 average time/residue: 0.6164 time to fit residues: 349.2901 Evaluate side-chains 404 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 297 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1926 VAL Chi-restraints excluded: chain A residue 1941 ARG Chi-restraints excluded: chain A residue 1943 HIS Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2168 LEU Chi-restraints excluded: chain A residue 2245 GLN Chi-restraints excluded: chain A residue 2314 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 934 CYS Chi-restraints excluded: chain B residue 1005 HIS Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1319 LEU Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1703 SER Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1760 ARG Chi-restraints excluded: chain B residue 1761 VAL Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1928 THR Chi-restraints excluded: chain B residue 1929 LYS Chi-restraints excluded: chain B residue 1961 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2088 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2103 ARG Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2114 ARG Chi-restraints excluded: chain B residue 2137 MET Chi-restraints excluded: chain B residue 2176 ILE Chi-restraints excluded: chain B residue 2182 VAL Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2226 ASP Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1994 GLU Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2244 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 871 ASP Chi-restraints excluded: chain C residue 934 CYS Chi-restraints excluded: chain C residue 959 GLU Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 995 LEU Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1369 ILE Chi-restraints excluded: chain C residue 1404 TYR Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1657 ILE Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1814 ILE Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 1864 THR Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 461 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 316 optimal weight: 0.4980 chunk 313 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 21 optimal weight: 0.0170 chunk 447 optimal weight: 6.9990 chunk 352 optimal weight: 8.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN A2190 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1384 ASN B1443 GLN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2190 HIS D1946 GLN C 664 HIS C 850 HIS ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1868 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.281381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.256370 restraints weight = 68719.319| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 2.37 r_work: 0.4580 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4457 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40398 Z= 0.167 Angle : 0.689 12.594 54727 Z= 0.353 Chirality : 0.046 0.207 6098 Planarity : 0.005 0.073 7043 Dihedral : 6.992 85.838 5551 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.64 % Allowed : 19.19 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.12), residues: 4863 helix: 0.56 (0.11), residues: 2141 sheet: 0.52 (0.17), residues: 834 loop : -1.76 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2221 TYR 0.031 0.002 TYR B 994 PHE 0.066 0.002 PHE B1011 TRP 0.035 0.002 TRP B2018 HIS 0.017 0.001 HIS B1005 Details of bonding type rmsd covalent geometry : bond 0.00382 (40398) covalent geometry : angle 0.68946 (54727) hydrogen bonds : bond 0.04243 ( 1918) hydrogen bonds : angle 5.11341 ( 5532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 335 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 864 MET cc_start: 0.2594 (tmt) cc_final: 0.1836 (ttm) REVERT: A 886 MET cc_start: 0.2973 (tmm) cc_final: 0.2513 (ttm) REVERT: A 922 MET cc_start: 0.0613 (tmm) cc_final: -0.1090 (pmm) REVERT: A 1009 CYS cc_start: 0.2100 (OUTLIER) cc_final: 0.1418 (p) REVERT: A 1021 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.2361 (mtm) REVERT: A 1147 MET cc_start: 0.1878 (mmm) cc_final: 0.1678 (mtt) REVERT: A 1307 MET cc_start: 0.2003 (ppp) cc_final: 0.0334 (mtt) REVERT: A 1483 MET cc_start: -0.2194 (ptp) cc_final: -0.3033 (tpp) REVERT: A 1745 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 1964 MET cc_start: 0.7185 (mtm) cc_final: 0.6700 (mtp) REVERT: A 1970 THR cc_start: 0.6799 (OUTLIER) cc_final: 0.6249 (p) REVERT: A 2168 LEU cc_start: 0.5258 (mm) cc_final: 0.4716 (pp) REVERT: B 697 MET cc_start: 0.3762 (tpt) cc_final: 0.0791 (mtm) REVERT: B 864 MET cc_start: 0.5475 (tpp) cc_final: 0.5244 (mmt) REVERT: B 903 MET cc_start: 0.4733 (mpp) cc_final: 0.3317 (mmt) REVERT: B 1066 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7608 (tt) REVERT: B 1385 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6203 (tpp-160) REVERT: B 1401 MET cc_start: 0.7284 (ppp) cc_final: 0.7081 (ppp) REVERT: B 1457 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6512 (tt) REVERT: B 1483 MET cc_start: 0.4616 (ttm) cc_final: 0.3201 (mmt) REVERT: B 1641 ASP cc_start: 0.7207 (p0) cc_final: 0.6994 (p0) REVERT: B 1688 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6806 (pp) REVERT: B 1962 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: B 2040 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 2114 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7500 (mmt90) REVERT: D 2003 ASN cc_start: 0.2967 (OUTLIER) cc_final: 0.0788 (m-40) REVERT: D 2011 ILE cc_start: 0.1482 (OUTLIER) cc_final: 0.0699 (mt) REVERT: D 2053 MET cc_start: -0.0065 (mtt) cc_final: -0.1353 (tmt) REVERT: D 2056 MET cc_start: 0.2329 (mmm) cc_final: 0.1920 (mmp) REVERT: D 2107 MET cc_start: 0.0731 (tpt) cc_final: -0.1421 (ttm) REVERT: D 2231 LYS cc_start: 0.3262 (OUTLIER) cc_final: 0.2645 (mtmm) REVERT: C 632 VAL cc_start: 0.2286 (m) cc_final: 0.2036 (m) REVERT: C 728 LYS cc_start: 0.3497 (mppt) cc_final: 0.2549 (tptt) REVERT: C 912 PRO cc_start: 0.3121 (Cg_exo) cc_final: 0.2910 (Cg_endo) REVERT: C 963 MET cc_start: 0.3985 (OUTLIER) cc_final: 0.3587 (tmt) REVERT: C 1386 MET cc_start: 0.3479 (mmm) cc_final: 0.2510 (ppp) REVERT: C 1401 MET cc_start: 0.2154 (mpp) cc_final: 0.1315 (pmm) REVERT: C 1418 ASP cc_start: 0.3393 (OUTLIER) cc_final: 0.2292 (t0) REVERT: C 1421 PHE cc_start: 0.3104 (m-10) cc_final: 0.2737 (m-10) REVERT: C 1489 GLU cc_start: 0.4126 (mm-30) cc_final: 0.3237 (tp30) REVERT: C 1631 MET cc_start: -0.0454 (tpt) cc_final: -0.4355 (mtm) REVERT: C 1731 ARG cc_start: 0.3050 (OUTLIER) cc_final: 0.1634 (tmt-80) REVERT: C 1788 LYS cc_start: 0.4567 (tppt) cc_final: 0.3508 (mmmt) REVERT: C 1795 GLU cc_start: 0.1954 (pm20) cc_final: 0.0839 (tp30) REVERT: C 1816 THR cc_start: 0.0882 (OUTLIER) cc_final: 0.0605 (t) outliers start: 115 outliers final: 60 residues processed: 424 average time/residue: 0.6785 time to fit residues: 357.0052 Evaluate side-chains 384 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1926 VAL Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 934 CYS Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1066 LEU Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1136 ASN Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1384 ASN Chi-restraints excluded: chain B residue 1385 ARG Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1703 SER Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1961 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2114 ARG Chi-restraints excluded: chain B residue 2128 PHE Chi-restraints excluded: chain B residue 2176 ILE Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2231 LYS Chi-restraints excluded: chain D residue 2244 ILE Chi-restraints excluded: chain C residue 934 CYS Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 119 optimal weight: 0.7980 chunk 455 optimal weight: 6.9990 chunk 117 optimal weight: 0.2980 chunk 318 optimal weight: 10.0000 chunk 468 optimal weight: 0.3980 chunk 466 optimal weight: 5.9990 chunk 439 optimal weight: 0.0270 chunk 196 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 415 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1287 HIS ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1843 ASN C 664 HIS ** C 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1868 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.281518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.256590 restraints weight = 68586.309| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 2.37 r_work: 0.4566 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 40398 Z= 0.180 Angle : 0.771 59.199 54727 Z= 0.414 Chirality : 0.047 0.665 6098 Planarity : 0.005 0.086 7043 Dihedral : 6.976 85.689 5551 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.32 % Allowed : 19.72 % Favored : 77.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.12), residues: 4863 helix: 0.59 (0.11), residues: 2141 sheet: 0.53 (0.17), residues: 835 loop : -1.74 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 992 TYR 0.029 0.002 TYR B 994 PHE 0.064 0.002 PHE B1011 TRP 0.030 0.002 TRP B2018 HIS 0.110 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00405 (40398) covalent geometry : angle 0.77074 (54727) hydrogen bonds : bond 0.04208 ( 1918) hydrogen bonds : angle 5.12037 ( 5532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9726 Ramachandran restraints generated. 4863 Oldfield, 0 Emsley, 4863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 310 time to evaluate : 1.637 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 864 MET cc_start: 0.2602 (tmt) cc_final: 0.1842 (ttm) REVERT: A 886 MET cc_start: 0.2964 (tmm) cc_final: 0.2480 (ttm) REVERT: A 922 MET cc_start: 0.0544 (tmm) cc_final: -0.1158 (pmm) REVERT: A 1009 CYS cc_start: 0.2053 (OUTLIER) cc_final: 0.1382 (p) REVERT: A 1021 MET cc_start: 0.4474 (OUTLIER) cc_final: 0.2374 (mtm) REVERT: A 1307 MET cc_start: 0.1995 (ppp) cc_final: 0.0291 (mtt) REVERT: A 1483 MET cc_start: -0.2180 (OUTLIER) cc_final: -0.3000 (tpp) REVERT: A 1745 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: A 1964 MET cc_start: 0.7153 (mtm) cc_final: 0.6665 (mtp) REVERT: A 1970 THR cc_start: 0.6755 (OUTLIER) cc_final: 0.6216 (p) REVERT: A 2146 HIS cc_start: 0.2996 (OUTLIER) cc_final: 0.2758 (t70) REVERT: A 2168 LEU cc_start: 0.5208 (mm) cc_final: 0.4716 (pp) REVERT: B 697 MET cc_start: 0.3774 (tpt) cc_final: 0.0830 (mtm) REVERT: B 864 MET cc_start: 0.5411 (tpp) cc_final: 0.5139 (mmt) REVERT: B 903 MET cc_start: 0.4678 (mpp) cc_final: 0.3314 (mmt) REVERT: B 1384 ASN cc_start: 0.6215 (OUTLIER) cc_final: 0.5982 (m-40) REVERT: B 1385 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6090 (tpp-160) REVERT: B 1401 MET cc_start: 0.7213 (ppp) cc_final: 0.6985 (ppp) REVERT: B 1457 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6473 (tt) REVERT: B 1483 MET cc_start: 0.4519 (ttm) cc_final: 0.3152 (mmt) REVERT: B 1688 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6530 (pp) REVERT: B 1962 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 2040 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 2114 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7409 (mmt90) REVERT: B 2190 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.6483 (p90) REVERT: D 2003 ASN cc_start: 0.2958 (OUTLIER) cc_final: 0.0771 (m-40) REVERT: D 2011 ILE cc_start: 0.1505 (OUTLIER) cc_final: 0.0733 (mt) REVERT: D 2053 MET cc_start: -0.0128 (mtt) cc_final: -0.1409 (tmt) REVERT: D 2056 MET cc_start: 0.2313 (mmm) cc_final: 0.1907 (mmp) REVERT: D 2107 MET cc_start: 0.0642 (tpt) cc_final: -0.1471 (ttm) REVERT: D 2231 LYS cc_start: 0.3223 (OUTLIER) cc_final: 0.2612 (mtmm) REVERT: C 632 VAL cc_start: 0.2279 (m) cc_final: 0.2021 (m) REVERT: C 728 LYS cc_start: 0.3462 (mppt) cc_final: 0.2534 (tptt) REVERT: C 912 PRO cc_start: 0.3115 (Cg_exo) cc_final: 0.2913 (Cg_endo) REVERT: C 963 MET cc_start: 0.3953 (OUTLIER) cc_final: 0.3498 (tmt) REVERT: C 1386 MET cc_start: 0.3460 (mmm) cc_final: 0.2525 (ppp) REVERT: C 1401 MET cc_start: 0.2171 (mpp) cc_final: 0.1335 (pmm) REVERT: C 1418 ASP cc_start: 0.3359 (OUTLIER) cc_final: 0.2242 (t0) REVERT: C 1421 PHE cc_start: 0.3051 (m-10) cc_final: 0.2731 (m-10) REVERT: C 1489 GLU cc_start: 0.4141 (mm-30) cc_final: 0.3260 (tp30) REVERT: C 1557 MET cc_start: 0.1535 (tpt) cc_final: 0.0613 (mpp) REVERT: C 1616 MET cc_start: -0.0052 (mtt) cc_final: -0.0527 (mtm) REVERT: C 1631 MET cc_start: -0.0350 (tpt) cc_final: -0.4332 (mtm) REVERT: C 1731 ARG cc_start: 0.3015 (OUTLIER) cc_final: 0.1619 (tmt-80) REVERT: C 1788 LYS cc_start: 0.4523 (tppt) cc_final: 0.3503 (mmmt) REVERT: C 1795 GLU cc_start: 0.1860 (pm20) cc_final: 0.0844 (tp30) REVERT: C 1816 THR cc_start: 0.0837 (OUTLIER) cc_final: 0.0559 (t) outliers start: 101 outliers final: 63 residues processed: 385 average time/residue: 0.6458 time to fit residues: 308.5262 Evaluate side-chains 386 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 302 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 CYS Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1483 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1592 SER Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1705 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1745 TYR Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1900 SER Chi-restraints excluded: chain A residue 1909 SER Chi-restraints excluded: chain A residue 1910 VAL Chi-restraints excluded: chain A residue 1926 VAL Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1943 HIS Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1994 GLU Chi-restraints excluded: chain A residue 2137 MET Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain B residue 868 CYS Chi-restraints excluded: chain B residue 922 MET Chi-restraints excluded: chain B residue 934 CYS Chi-restraints excluded: chain B residue 1062 ILE Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1128 THR Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain B residue 1291 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1384 ASN Chi-restraints excluded: chain B residue 1385 ARG Chi-restraints excluded: chain B residue 1457 LEU Chi-restraints excluded: chain B residue 1517 ILE Chi-restraints excluded: chain B residue 1577 TYR Chi-restraints excluded: chain B residue 1635 THR Chi-restraints excluded: chain B residue 1688 ILE Chi-restraints excluded: chain B residue 1703 SER Chi-restraints excluded: chain B residue 1717 SER Chi-restraints excluded: chain B residue 1807 SER Chi-restraints excluded: chain B residue 1876 HIS Chi-restraints excluded: chain B residue 1929 LYS Chi-restraints excluded: chain B residue 1947 LYS Chi-restraints excluded: chain B residue 1961 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1989 GLU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2031 LYS Chi-restraints excluded: chain B residue 2035 ARG Chi-restraints excluded: chain B residue 2040 LEU Chi-restraints excluded: chain B residue 2088 LEU Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2113 SER Chi-restraints excluded: chain B residue 2114 ARG Chi-restraints excluded: chain B residue 2128 PHE Chi-restraints excluded: chain B residue 2176 ILE Chi-restraints excluded: chain B residue 2190 HIS Chi-restraints excluded: chain B residue 2213 THR Chi-restraints excluded: chain B residue 2329 THR Chi-restraints excluded: chain D residue 1802 MET Chi-restraints excluded: chain D residue 2003 ASN Chi-restraints excluded: chain D residue 2011 ILE Chi-restraints excluded: chain D residue 2026 THR Chi-restraints excluded: chain D residue 2199 LYS Chi-restraints excluded: chain D residue 2231 LYS Chi-restraints excluded: chain D residue 2244 ILE Chi-restraints excluded: chain C residue 934 CYS Chi-restraints excluded: chain C residue 963 MET Chi-restraints excluded: chain C residue 972 VAL Chi-restraints excluded: chain C residue 1029 PHE Chi-restraints excluded: chain C residue 1035 THR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1613 TRP Chi-restraints excluded: chain C residue 1665 THR Chi-restraints excluded: chain C residue 1685 THR Chi-restraints excluded: chain C residue 1731 ARG Chi-restraints excluded: chain C residue 1816 THR Chi-restraints excluded: chain C residue 2053 MET Chi-restraints excluded: chain C residue 2069 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 180 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 367 optimal weight: 6.9990 chunk 446 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 470 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 HIS ** B1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1843 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 850 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1868 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.281453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.254389 restraints weight = 68854.140| |-----------------------------------------------------------------------------| r_work (start): 0.4850 rms_B_bonded: 2.54 r_work: 0.4558 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.4457 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 40398 Z= 0.180 Angle : 0.771 59.179 54727 Z= 0.414 Chirality : 0.047 0.665 6098 Planarity : 0.005 0.086 7043 Dihedral : 6.976 85.689 5551 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.98 % Allowed : 20.02 % Favored : 78.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.12), residues: 4863 helix: 0.59 (0.11), residues: 2141 sheet: 0.53 (0.17), residues: 835 loop : -1.74 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 992 TYR 0.029 0.002 TYR B 994 PHE 0.064 0.002 PHE B1011 TRP 0.030 0.002 TRP B2018 HIS 0.109 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00405 (40398) covalent geometry : angle 0.77067 (54727) hydrogen bonds : bond 0.04208 ( 1918) hydrogen bonds : angle 5.12038 ( 5532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15679.00 seconds wall clock time: 267 minutes 14.85 seconds (16034.85 seconds total)