Starting phenix.real_space_refine on Sun Aug 24 09:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl1_38434/08_2025/8xl1_38434.cif" } resolution = 2.57 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= 0.109 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 6 5.49 5 S 100 5.16 5 C 11736 2.51 5 N 3203 2.21 5 O 3432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18477 Number of models: 1 Model: "" Number of chains: 4 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: 6068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 6068 Classifications: {'peptide': 758} Link IDs: {'PTRANS': 40, 'TRANS': 717} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 3.65, per 1000 atoms: 0.20 Number of scatterers: 18477 At special positions: 0 Unit cell: (115.271, 120.658, 200.378, 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 100 16.00 P 6 15.00 O 3432 8.00 N 3203 7.00 C 11736 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: 1.18 Conformation dependent library (CDL) restraints added in 607.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 17 sheets defined 48.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 627 through 657 Processing helix chain 'A' and resid 850 through 865 removed outlier: 3.910A 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 956 through 965 removed outlier: 3.691A pdb=" N VAL A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.593A pdb=" N GLY A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1021 through 1033 removed outlier: 3.885A pdb=" N GLN A1033 " --> pdb=" O PHE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1047 removed outlier: 3.534A pdb=" N GLN A1047 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 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 removed outlier: 3.572A pdb=" N ARG A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1107 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: 3.508A pdb=" N ALA A1148 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1248 removed outlier: 4.095A 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: 4.058A 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 1463 removed outlier: 3.848A 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 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 1627 through 1631 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 1760 through 1765 removed outlier: 5.520A pdb=" N ALA A1763 " --> pdb=" O ARG A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1814 removed outlier: 3.869A pdb=" N ASN A1812 " --> pdb=" O SER A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1836 removed outlier: 3.597A 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 1900 Processing helix chain 'A' and resid 1934 through 1939 Processing helix chain 'A' and resid 2019 through 2037 Processing helix chain 'A' and resid 2052 through 2058 Processing helix chain 'A' and resid 2059 through 2072 removed outlier: 4.124A pdb=" N PHE A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A2068 " --> pdb=" O GLY A2064 " (cutoff:3.500A) Processing helix chain 'A' and resid 2091 through 2093 No H-bonds generated for 'chain 'A' and resid 2091 through 2093' Processing helix chain 'A' and resid 2097 through 2101 removed outlier: 3.504A pdb=" N ASN A2101 " --> pdb=" O SER A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2119 through 2128 removed outlier: 3.517A 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 Processing helix chain 'A' and resid 2175 through 2189 Processing helix chain 'A' and resid 2192 through 2200 Processing helix chain 'A' and resid 2210 through 2236 removed outlier: 3.608A 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 2258 through 2261 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: 4.004A pdb=" N ILE A2320 " --> pdb=" O MET A2316 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A2321 " --> pdb=" O ASP A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2327 through 2337 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 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 1627 through 1630 Processing helix chain 'B' and resid 1692 through 1710 Processing helix chain 'B' and resid 1727 through 1734 Processing helix chain 'B' and resid 1743 through 1746 Processing helix chain 'B' and resid 1754 through 1759 Processing helix chain 'B' and resid 1760 through 1765 removed outlier: 5.514A pdb=" N ALA B1763 " --> pdb=" O ARG B1760 " (cutoff:3.500A) Processing helix chain 'B' and resid 1794 through 1812 removed outlier: 3.986A pdb=" N ASN B1812 " --> pdb=" O SER B1808 " (cutoff:3.500A) Processing helix chain 'B' and resid 1826 through 1836 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 1900 Processing helix chain 'B' and resid 1933 through 1939 removed outlier: 4.280A pdb=" N MET B1937 " --> pdb=" O ASP B1933 " (cutoff:3.500A) Processing helix chain 'B' and resid 2019 through 2037 Processing helix chain 'B' and resid 2052 through 2058 Processing helix chain 'B' and resid 2059 through 2072 removed outlier: 3.824A pdb=" N PHE B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B2068 " --> pdb=" O GLY B2064 " (cutoff:3.500A) Processing helix chain 'B' and resid 2090 through 2095 removed outlier: 3.572A pdb=" N VAL B2094 " --> pdb=" O GLY B2090 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B2095 " --> pdb=" O GLY B2091 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2090 through 2095' Processing helix chain 'B' and resid 2119 through 2128 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 2175 removed outlier: 3.573A pdb=" N ARG B2161 " --> pdb=" O SER B2157 " (cutoff:3.500A) Processing helix chain 'B' and resid 2175 through 2189 removed outlier: 3.545A pdb=" N TYR B2179 " --> pdb=" O LEU B2175 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2200 removed outlier: 3.553A pdb=" N MET B2196 " --> pdb=" O THR B2192 " (cutoff:3.500A) Processing helix chain 'B' and resid 2210 through 2236 removed outlier: 3.760A 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 2258 through 2261 Processing helix chain 'B' and resid 2266 through 2280 removed outlier: 3.662A pdb=" N GLU B2280 " --> pdb=" O LYS B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2311 Processing helix chain 'B' and resid 2314 through 2322 removed outlier: 3.827A pdb=" N ILE B2320 " --> pdb=" O MET B2316 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B2321 " --> pdb=" O ASP B2317 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B2322 " --> pdb=" O SER B2318 " (cutoff:3.500A) Processing helix chain 'B' and resid 2327 through 2337 Processing sheet with id=AA1, first strand: chain 'A' and resid 670 through 676 Processing sheet with id=AA2, first strand: chain 'A' and resid 1162 through 1170 removed outlier: 6.721A pdb=" N GLN A1181 " --> pdb=" O ASN A1164 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A1166 " --> pdb=" O GLU A1179 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A1179 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A1168 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A1177 " --> pdb=" O HIS A1168 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS A1176 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A1238 " --> pdb=" O CYS A1176 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A1233 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN A1290 " --> pdb=" O MET A1233 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A1235 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A1292 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A1237 " --> pdb=" O ALA A1292 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N LYS A1294 " --> pdb=" O VAL A1237 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE A1239 " --> pdb=" O LYS A1294 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS A1287 " --> pdb=" O ARG A1326 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR A1328 " --> pdb=" O HIS A1287 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A1289 " --> pdb=" O THR A1328 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU A1330 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A1291 " --> pdb=" O LEU A1330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1389 through 1394 removed outlier: 4.819A pdb=" N LEU A1403 " --> pdb=" O ILE A1394 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A1508 " --> pdb=" O ASN A1471 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE A1473 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLN A1510 " --> pdb=" O ILE A1473 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N LEU A1475 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A1512 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A1477 " --> pdb=" O GLU A1512 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A1514 " --> pdb=" O PHE A1477 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN A1516 " --> pdb=" O PRO A1479 " (cutoff:3.500A) removed outlier: 4.464A 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: 4.277A pdb=" N ALA A1661 " --> pdb=" O LEU A1637 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A1639 " --> pdb=" O MET A1659 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N MET A1659 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ILE A1714 " --> pdb=" O ASP A1676 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A1678 " --> pdb=" O ILE A1714 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A1716 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A1680 " --> pdb=" O VAL A1716 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.852A pdb=" N TYR A1750 " --> pdb=" O ALA A1737 " (cutoff:3.500A) removed outlier: 16.738A pdb=" N ARG A1749 " --> pdb=" O ASP A1784 " (cutoff:3.500A) removed outlier: 12.196A pdb=" N ASP A1784 " --> pdb=" O ARG A1749 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU A1751 " --> pdb=" O ILE A1782 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER A1778 " --> pdb=" O ASP A1774 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP A1774 " --> pdb=" O SER A1778 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR A1780 " --> pdb=" O VAL A1772 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1772 " --> pdb=" O TYR A1780 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE A1782 " --> pdb=" O GLU A1770 " (cutoff:3.500A) removed outlier: 6.259A 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: 6.339A 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 1940 through 1942 Processing sheet with id=AA8, first strand: chain 'A' and resid 1961 through 1962 removed outlier: 7.860A pdb=" N MET A2041 " --> pdb=" O PRO A1982 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY A1984 " --> pdb=" O MET A2041 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE A2043 " --> pdb=" O GLY A1984 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A1986 " --> pdb=" O PHE A2043 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A2206 " --> pdb=" O MET A2107 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A2109 " --> pdb=" O LEU A2206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1993 through 1997 Processing sheet with id=AB1, first strand: chain 'A' and resid 2086 through 2089 removed outlier: 6.472A pdb=" N ALA A2086 " --> pdb=" O ARG A2114 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N SER A2116 " --> pdb=" O ALA A2086 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A2088 " --> pdb=" O SER A2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1645 through 1648 removed outlier: 4.308A pdb=" N ALA B1661 " --> pdb=" O LEU B1637 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU B1639 " --> pdb=" O MET B1659 " (cutoff:3.500A) removed outlier: 11.636A pdb=" N MET B1659 " --> pdb=" O LEU B1639 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ILE B1714 " --> pdb=" O ASP B1676 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B1678 " --> pdb=" O ILE B1714 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B1716 " --> pdb=" O ILE B1678 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B1680 " --> pdb=" O VAL B1716 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG B1713 " --> pdb=" O ILE B1817 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B1819 " --> pdb=" O ARG B1713 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR B1715 " --> pdb=" O LEU B1819 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1735 through 1738 removed outlier: 6.620A pdb=" N HIS B1735 " --> pdb=" O LEU B1751 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B1751 " --> pdb=" O HIS B1735 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B1737 " --> pdb=" O ARG B1749 " (cutoff:3.500A) removed outlier: 17.290A pdb=" N ARG B1749 " --> pdb=" O ASP B1784 " (cutoff:3.500A) removed outlier: 12.506A pdb=" N ASP B1784 " --> pdb=" O ARG B1749 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B1751 " --> pdb=" O ILE B1782 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER B1778 " --> pdb=" O ASP B1774 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B1774 " --> pdb=" O SER B1778 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR B1780 " --> pdb=" O VAL B1772 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B1772 " --> pdb=" O TYR B1780 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE B1782 " --> pdb=" O GLU B1770 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU B1770 " --> pdb=" O ILE B1782 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1824 through 1825 removed outlier: 6.140A pdb=" N ALA B1824 " --> pdb=" O ILE B1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1940 through 1942 Processing sheet with id=AB6, first strand: chain 'B' and resid 1961 through 1962 removed outlier: 7.778A pdb=" N MET B2041 " --> pdb=" O PRO B1982 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLY B1984 " --> pdb=" O MET B2041 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE B2043 " --> pdb=" O GLY B1984 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1986 " --> pdb=" O PHE B2043 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N ASP B2204 " --> pdb=" O MET B2105 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET B2107 " --> pdb=" O ASP B2204 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU B2206 " --> pdb=" O MET B2107 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B2109 " --> pdb=" O LEU B2206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1993 through 1997 Processing sheet with id=AB8, first strand: chain 'B' and resid 2086 through 2089 removed outlier: 6.379A pdb=" N ALA B2086 " --> pdb=" O ARG B2114 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER B2116 " --> pdb=" O ALA B2086 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B2088 " --> pdb=" O SER B2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 917 hydrogen bonds defined for protein. 2652 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: 3.19 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3212 1.32 - 1.44: 4899 1.44 - 1.57: 10585 1.57 - 1.69: 13 1.69 - 1.81: 171 Bond restraints: 18880 Sorted by residual: bond pdb=" C5A ACO A2501 " pdb=" C6A ACO A2501 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5A ACO B2501 " pdb=" C6A ACO B2501 " 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 B2501 " pdb=" C5A ACO B2501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.20e-02 6.94e+03 4.83e+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 4.75e+01 bond pdb=" C2P ACO A2501 " pdb=" S1P ACO A2501 " ideal model delta sigma weight residual 1.818 1.762 0.056 1.00e-02 1.00e+04 3.14e+01 ... (remaining 18875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 25306 3.27 - 6.54: 255 6.54 - 9.80: 21 9.80 - 13.07: 1 13.07 - 16.34: 4 Bond angle restraints: 25587 Sorted by residual: angle pdb=" P1A ACO A2501 " pdb=" O3A ACO A2501 " pdb=" P2A ACO A2501 " ideal model delta sigma weight residual 136.83 120.49 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" P1A ACO B2501 " pdb=" O3A ACO B2501 " pdb=" P2A ACO B2501 " ideal model delta sigma weight residual 136.83 120.50 16.33 1.00e+00 1.00e+00 2.67e+02 angle pdb=" C5A ACO B2501 " pdb=" C4A ACO B2501 " pdb=" N3A ACO B2501 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.69e+01 angle pdb=" C5A ACO A2501 " pdb=" C4A ACO A2501 " pdb=" N3A ACO A2501 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.66e+01 angle pdb=" N3A ACO B2501 " pdb=" C4A ACO B2501 " pdb=" N9A ACO B2501 " ideal model delta sigma weight residual 127.04 135.02 -7.98 1.15e+00 7.59e-01 4.83e+01 ... (remaining 25582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 10805 17.62 - 35.23: 482 35.23 - 52.85: 107 52.85 - 70.47: 42 70.47 - 88.08: 11 Dihedral angle restraints: 11447 sinusoidal: 4789 harmonic: 6658 Sorted by residual: 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 -135.72 -44.28 0 5.00e+00 4.00e-02 7.84e+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 -136.16 -43.84 0 5.00e+00 4.00e-02 7.69e+01 dihedral pdb=" CA THR A1241 " pdb=" C THR A1241 " pdb=" N PHE A1242 " pdb=" CA PHE A1242 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 ... (remaining 11444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1793 0.040 - 0.080: 723 0.080 - 0.120: 234 0.120 - 0.160: 73 0.160 - 0.200: 8 Chirality restraints: 2831 Sorted by residual: chirality pdb=" CAP ACO B2501 " pdb=" C9P ACO B2501 " pdb=" CBP ACO B2501 " pdb=" OAP ACO B2501 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 1.00e+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 9.94e-01 chirality pdb=" CA SER B1720 " pdb=" N SER B1720 " pdb=" C SER B1720 " pdb=" CB SER B1720 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 2828 not shown) Planarity restraints: 3293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO A2501 " -0.304 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C9P ACO A2501 " 0.069 2.00e-02 2.50e+03 pdb=" CAP ACO A2501 " 0.002 2.00e-02 2.50e+03 pdb=" N8P ACO A2501 " 0.445 2.00e-02 2.50e+03 pdb=" O9P ACO A2501 " -0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO B2501 " -0.281 2.00e-02 2.50e+03 2.35e-01 6.88e+02 pdb=" C5P ACO B2501 " 0.077 2.00e-02 2.50e+03 pdb=" C6P ACO B2501 " -0.185 2.00e-02 2.50e+03 pdb=" N4P ACO B2501 " 0.395 2.00e-02 2.50e+03 pdb=" O5P ACO B2501 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO A2501 " 0.231 2.00e-02 2.50e+03 1.91e-01 4.57e+02 pdb=" C5P ACO A2501 " -0.064 2.00e-02 2.50e+03 pdb=" C6P ACO A2501 " 0.163 2.00e-02 2.50e+03 pdb=" N4P ACO A2501 " -0.314 2.00e-02 2.50e+03 pdb=" O5P ACO A2501 " -0.016 2.00e-02 2.50e+03 ... (remaining 3290 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3096 2.77 - 3.30: 17529 3.30 - 3.84: 30052 3.84 - 4.37: 37360 4.37 - 4.90: 62914 Nonbonded interactions: 150951 Sorted by model distance: nonbonded pdb=" OH TYR A1745 " pdb=" O PHE B2174 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A2050 " pdb=" OD2 ASP A2055 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU B1728 " pdb=" NH1 ARG B1731 " model vdw 2.261 3.120 nonbonded pdb=" O ASP B1956 " pdb=" OG SER B1959 " model vdw 2.262 3.040 nonbonded pdb=" NZ LYS B2031 " pdb=" OE1 GLU B2073 " model vdw 2.308 3.120 ... (remaining 150946 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.870 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 18880 Z= 0.363 Angle : 0.869 16.341 25587 Z= 0.510 Chirality : 0.050 0.200 2831 Planarity : 0.009 0.261 3293 Dihedral : 11.723 88.082 7153 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.35 % Favored : 96.21 % Rotamer: Outliers : 1.29 % Allowed : 1.24 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.45 (0.17), residues: 2271 helix: -0.01 (0.15), residues: 1008 sheet: 0.87 (0.25), residues: 386 loop : -1.06 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1833 TYR 0.016 0.002 TYR A1538 PHE 0.026 0.002 PHE B1734 TRP 0.033 0.003 TRP B2018 HIS 0.012 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00782 (18880) covalent geometry : angle 0.86879 (25587) hydrogen bonds : bond 0.15511 ( 917) hydrogen bonds : angle 6.74995 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 350 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1131 PHE cc_start: 0.5913 (m-80) cc_final: 0.5634 (m-80) REVERT: A 1444 ASN cc_start: 0.6008 (m-40) cc_final: 0.5498 (p0) REVERT: A 1477 PHE cc_start: 0.6671 (m-80) cc_final: 0.6338 (m-80) REVERT: A 1558 PHE cc_start: 0.6189 (m-80) cc_final: 0.5804 (m-80) REVERT: A 1688 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7366 (pt) REVERT: A 1731 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7508 (ptp-170) REVERT: A 1823 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8223 (ptt-90) REVERT: A 1962 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: A 2000 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6624 (t0) REVERT: A 2040 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8609 (tp) REVERT: A 2225 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6104 (mm-30) REVERT: A 2249 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6422 (mtp180) REVERT: A 2305 ARG cc_start: 0.4912 (mtm180) cc_final: 0.4433 (mtt180) REVERT: B 1962 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6228 (tt0) REVERT: B 2035 ARG cc_start: 0.7145 (mtt90) cc_final: 0.6638 (mmp80) REVERT: B 2119 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6852 (mp0) REVERT: B 2204 ASP cc_start: 0.6168 (t0) cc_final: 0.5738 (t0) REVERT: B 2247 MET cc_start: 0.6583 (mtp) cc_final: 0.6238 (mtp) REVERT: B 2322 MET cc_start: 0.4899 (mtm) cc_final: 0.3786 (ptt) outliers start: 26 outliers final: 2 residues processed: 372 average time/residue: 0.6938 time to fit residues: 285.3068 Evaluate side-chains 209 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1731 ARG Chi-restraints excluded: chain A residue 1823 ARG Chi-restraints excluded: chain A residue 1888 ASP Chi-restraints excluded: chain A residue 1962 GLU Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2040 LEU Chi-restraints excluded: chain A residue 2249 ARG Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 2011 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1068 GLN A1188 HIS A1555 GLN A1591 GLN A1619 GLN B1943 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.233213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.174807 restraints weight = 25902.999| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.15 r_work: 0.3876 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18880 Z= 0.136 Angle : 0.595 9.771 25587 Z= 0.317 Chirality : 0.045 0.240 2831 Planarity : 0.004 0.040 3293 Dihedral : 8.379 85.746 2646 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 1.73 % Allowed : 9.74 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.51 (0.17), residues: 2271 helix: 1.13 (0.16), residues: 1022 sheet: 1.07 (0.25), residues: 385 loop : -0.94 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2047 TYR 0.018 0.001 TYR A1027 PHE 0.020 0.002 PHE A2174 TRP 0.021 0.001 TRP B1662 HIS 0.005 0.001 HIS A2190 Details of bonding type rmsd covalent geometry : bond 0.00276 (18880) covalent geometry : angle 0.59540 (25587) hydrogen bonds : bond 0.04645 ( 917) hydrogen bonds : angle 4.88710 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.2967 (OUTLIER) cc_final: 0.2685 (tpt) REVERT: A 998 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6888 (tp30) REVERT: A 1110 MET cc_start: 0.0514 (OUTLIER) cc_final: -0.0317 (ptp) REVERT: A 1131 PHE cc_start: 0.5943 (m-80) cc_final: 0.5602 (m-80) REVERT: A 1253 MET cc_start: 0.2529 (pp-130) cc_final: 0.1624 (ptm) REVERT: A 1490 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7146 (tm-30) REVERT: A 1510 GLN cc_start: 0.7510 (mt0) cc_final: 0.7119 (mp10) REVERT: A 1533 THR cc_start: 0.7388 (m) cc_final: 0.7110 (p) REVERT: A 1545 TYR cc_start: 0.5620 (m-80) cc_final: 0.5211 (m-80) REVERT: A 1557 MET cc_start: 0.6059 (mmt) cc_final: 0.5689 (mmm) REVERT: A 1558 PHE cc_start: 0.5740 (m-80) cc_final: 0.5161 (m-80) REVERT: A 1688 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6535 (tt) REVERT: A 1830 TYR cc_start: 0.8470 (m-80) cc_final: 0.8133 (m-80) REVERT: A 1962 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: A 2000 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6612 (t0) REVERT: A 2040 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8891 (tp) REVERT: A 2137 MET cc_start: 0.8001 (mtt) cc_final: 0.7303 (mtt) REVERT: A 2138 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.6719 (mmm160) REVERT: A 2225 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7167 (mm-30) REVERT: B 1589 GLN cc_start: 0.4981 (tt0) cc_final: 0.4754 (mt0) REVERT: B 1749 ARG cc_start: 0.6630 (ptp90) cc_final: 0.6178 (ptt-90) REVERT: B 1889 PHE cc_start: 0.6897 (t80) cc_final: 0.6443 (m-80) REVERT: B 1919 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6617 (mm) REVERT: B 1962 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: B 2035 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7621 (mmp80) REVERT: B 2053 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7970 (tpt) REVERT: B 2119 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7145 (mp0) REVERT: B 2137 MET cc_start: 0.4377 (mtt) cc_final: 0.4036 (mtp) REVERT: B 2204 ASP cc_start: 0.6926 (t0) cc_final: 0.6573 (m-30) REVERT: B 2243 GLN cc_start: 0.6419 (mp10) cc_final: 0.6121 (mt0) REVERT: B 2247 MET cc_start: 0.6666 (mtp) cc_final: 0.6327 (mtp) REVERT: B 2322 MET cc_start: 0.4108 (mtm) cc_final: 0.3301 (ptt) outliers start: 35 outliers final: 11 residues processed: 243 average time/residue: 0.5839 time to fit residues: 158.5526 Evaluate side-chains 197 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1616 MET Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1962 GLU Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2040 LEU Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2178 ILE Chi-restraints excluded: chain B residue 1592 SER Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1660 VAL Chi-restraints excluded: chain B residue 1919 ILE Chi-restraints excluded: chain B residue 1943 HIS Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 2011 ILE Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2296 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 123 optimal weight: 1.9990 chunk 219 optimal weight: 0.2980 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 0.0980 chunk 187 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1315 ASN A1619 GLN A2245 GLN B1943 HIS B2190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.231698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172060 restraints weight = 26093.744| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.00 r_work: 0.3834 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18880 Z= 0.118 Angle : 0.556 11.666 25587 Z= 0.292 Chirality : 0.043 0.191 2831 Planarity : 0.004 0.042 3293 Dihedral : 7.715 83.575 2632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 11.03 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.18), residues: 2271 helix: 1.36 (0.16), residues: 1025 sheet: 1.26 (0.26), residues: 386 loop : -0.98 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1080 TYR 0.013 0.001 TYR A2299 PHE 0.019 0.001 PHE A1355 TRP 0.014 0.001 TRP B2018 HIS 0.021 0.001 HIS B1943 Details of bonding type rmsd covalent geometry : bond 0.00251 (18880) covalent geometry : angle 0.55550 (25587) hydrogen bonds : bond 0.04192 ( 917) hydrogen bonds : angle 4.64208 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.3192 (OUTLIER) cc_final: 0.2979 (tpt) REVERT: A 1031 HIS cc_start: 0.5135 (t70) cc_final: 0.4879 (t-170) REVERT: A 1253 MET cc_start: 0.2993 (pp-130) cc_final: 0.2267 (ptm) REVERT: A 1385 ARG cc_start: 0.4571 (ttm-80) cc_final: 0.4288 (ttm-80) REVERT: A 1449 LEU cc_start: 0.7307 (mt) cc_final: 0.6880 (tm) REVERT: A 1510 GLN cc_start: 0.7556 (mt0) cc_final: 0.7145 (mp10) REVERT: A 1557 MET cc_start: 0.5920 (mmt) cc_final: 0.5604 (mmm) REVERT: A 1558 PHE cc_start: 0.5509 (m-80) cc_final: 0.5032 (m-80) REVERT: A 1571 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5701 (mmm) REVERT: A 1742 GLU cc_start: 0.6184 (mp0) cc_final: 0.4983 (tp30) REVERT: A 1760 ARG cc_start: 0.6786 (ptt90) cc_final: 0.6463 (ptt90) REVERT: A 1830 TYR cc_start: 0.8579 (m-80) cc_final: 0.8255 (m-80) REVERT: A 2000 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6671 (t0) REVERT: A 2137 MET cc_start: 0.7873 (mtt) cc_final: 0.7351 (mtt) REVERT: A 2138 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.6935 (mmm160) REVERT: A 2305 ARG cc_start: 0.4978 (mtm180) cc_final: 0.4713 (mtt180) REVERT: B 1589 GLN cc_start: 0.5120 (tt0) cc_final: 0.4799 (mt0) REVERT: B 1648 MET cc_start: 0.6931 (mtp) cc_final: 0.6684 (mtm) REVERT: B 1749 ARG cc_start: 0.6958 (ptp90) cc_final: 0.6486 (ptt-90) REVERT: B 1889 PHE cc_start: 0.7058 (t80) cc_final: 0.6596 (m-80) REVERT: B 1919 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6505 (mm) REVERT: B 1962 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: B 2035 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7705 (mmp80) REVERT: B 2053 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.8030 (tpt) REVERT: B 2101 ASN cc_start: 0.7911 (t0) cc_final: 0.7633 (t160) REVERT: B 2119 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7291 (mp0) REVERT: B 2137 MET cc_start: 0.4526 (mtt) cc_final: 0.4197 (mtp) REVERT: B 2204 ASP cc_start: 0.7023 (t0) cc_final: 0.6797 (t0) REVERT: B 2247 MET cc_start: 0.6989 (mtp) cc_final: 0.6688 (mtp) REVERT: B 2322 MET cc_start: 0.4131 (mtm) cc_final: 0.3635 (ptt) outliers start: 42 outliers final: 14 residues processed: 223 average time/residue: 0.5529 time to fit residues: 138.2018 Evaluate side-chains 190 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 1110 MET Chi-restraints excluded: chain A residue 1571 MET Chi-restraints excluded: chain A residue 1616 MET Chi-restraints excluded: chain A residue 1648 MET Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2178 ILE Chi-restraints excluded: chain B residue 1592 SER Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1919 ILE Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 190 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 ASN A1619 GLN A1768 HIS A1868 GLN A2245 GLN A2324 GLN B1876 HIS B2190 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.224702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163544 restraints weight = 25742.799| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.20 r_work: 0.3752 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18880 Z= 0.228 Angle : 0.707 12.567 25587 Z= 0.371 Chirality : 0.048 0.252 2831 Planarity : 0.006 0.074 3293 Dihedral : 7.810 84.860 2625 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 3.17 % Allowed : 11.03 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.21 (0.17), residues: 2271 helix: 0.88 (0.16), residues: 1033 sheet: 1.00 (0.25), residues: 389 loop : -1.18 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1080 TYR 0.026 0.002 TYR B2081 PHE 0.032 0.002 PHE B1893 TRP 0.023 0.003 TRP B2018 HIS 0.012 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00531 (18880) covalent geometry : angle 0.70706 (25587) hydrogen bonds : bond 0.05343 ( 917) hydrogen bonds : angle 4.87609 ( 2652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 MET cc_start: 0.1715 (mmt) cc_final: 0.1454 (mmm) REVERT: A 1021 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.3623 (tpt) REVERT: A 1076 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.5131 (tmtt) REVERT: A 1131 PHE cc_start: 0.5963 (m-80) cc_final: 0.5624 (m-80) REVERT: A 1253 MET cc_start: 0.2980 (pp-130) cc_final: 0.2368 (ptm) REVERT: A 1385 ARG cc_start: 0.4267 (ttm-80) cc_final: 0.3985 (ttm-80) REVERT: A 1447 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6209 (mm-30) REVERT: A 1449 LEU cc_start: 0.7334 (mt) cc_final: 0.7011 (tm) REVERT: A 1477 PHE cc_start: 0.5337 (m-80) cc_final: 0.5073 (m-80) REVERT: A 1510 GLN cc_start: 0.7576 (mt0) cc_final: 0.7322 (mp10) REVERT: A 1557 MET cc_start: 0.5986 (mmt) cc_final: 0.5710 (mmm) REVERT: A 1558 PHE cc_start: 0.5498 (m-80) cc_final: 0.5097 (m-80) REVERT: A 1742 GLU cc_start: 0.6360 (mp0) cc_final: 0.5092 (tp30) REVERT: A 1830 TYR cc_start: 0.8624 (m-80) cc_final: 0.8248 (m-80) REVERT: A 2000 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6589 (t0) REVERT: A 2125 GLU cc_start: 0.8045 (tt0) cc_final: 0.7768 (tt0) REVERT: A 2190 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6710 (p-80) REVERT: A 2230 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6908 (ptpp) REVERT: A 2305 ARG cc_start: 0.5560 (mtm180) cc_final: 0.4962 (mtt180) REVERT: B 1856 LYS cc_start: 0.8206 (mttm) cc_final: 0.7831 (ttmm) REVERT: B 1962 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: B 2035 ARG cc_start: 0.8132 (mtt90) cc_final: 0.7785 (mmp80) REVERT: B 2047 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7321 (mtm180) REVERT: B 2119 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7554 (mp0) REVERT: B 2295 ILE cc_start: 0.5773 (mm) cc_final: 0.5451 (pt) outliers start: 64 outliers final: 13 residues processed: 245 average time/residue: 0.5506 time to fit residues: 150.7848 Evaluate side-chains 202 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2190 HIS Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1909 SER Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 2047 ARG Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2099 SER Chi-restraints excluded: chain B residue 2124 VAL Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2190 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 39 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1619 GLN B1765 ASN B1914 ASN B1943 HIS B2190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.228553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.170451 restraints weight = 26599.778| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.73 r_work: 0.3875 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18880 Z= 0.121 Angle : 0.569 11.925 25587 Z= 0.295 Chirality : 0.044 0.274 2831 Planarity : 0.004 0.042 3293 Dihedral : 7.432 80.556 2625 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 2.42 % Allowed : 13.06 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 (0.18), residues: 2271 helix: 1.19 (0.16), residues: 1034 sheet: 1.04 (0.26), residues: 394 loop : -1.16 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2297 TYR 0.012 0.001 TYR B1901 PHE 0.018 0.001 PHE A1355 TRP 0.022 0.001 TRP B2018 HIS 0.030 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00262 (18880) covalent geometry : angle 0.56890 (25587) hydrogen bonds : bond 0.03956 ( 917) hydrogen bonds : angle 4.55771 ( 2652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 MET cc_start: 0.1744 (mmt) cc_final: 0.1522 (mmm) REVERT: A 1021 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.3394 (mmp) REVERT: A 1076 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.5055 (tmtt) REVERT: A 1131 PHE cc_start: 0.5917 (m-80) cc_final: 0.5642 (m-80) REVERT: A 1253 MET cc_start: 0.2970 (pp-130) cc_final: 0.2383 (ptm) REVERT: A 1401 MET cc_start: 0.4628 (ppp) cc_final: 0.4361 (ppp) REVERT: A 1447 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6372 (mm-30) REVERT: A 1449 LEU cc_start: 0.7379 (mt) cc_final: 0.7067 (tm) REVERT: A 1454 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6658 (mmm) REVERT: A 1510 GLN cc_start: 0.7249 (mt0) cc_final: 0.6975 (mp10) REVERT: A 1557 MET cc_start: 0.5939 (mmt) cc_final: 0.5735 (mmm) REVERT: A 1568 LEU cc_start: 0.6774 (tp) cc_final: 0.6346 (tt) REVERT: A 1584 GLN cc_start: 0.7812 (tp40) cc_final: 0.7606 (tp40) REVERT: A 1742 GLU cc_start: 0.6397 (mp0) cc_final: 0.5221 (tp30) REVERT: A 1830 TYR cc_start: 0.8647 (m-80) cc_final: 0.8245 (m-80) REVERT: A 2000 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6457 (t0) REVERT: A 2137 MET cc_start: 0.7812 (mtt) cc_final: 0.7426 (mtt) REVERT: A 2190 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: A 2197 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.6908 (tp40) REVERT: A 2230 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6855 (ptpp) REVERT: A 2243 GLN cc_start: 0.7970 (mp10) cc_final: 0.7738 (mp-120) REVERT: A 2305 ARG cc_start: 0.5551 (mtm180) cc_final: 0.4856 (mtt-85) REVERT: B 1604 MET cc_start: 0.6955 (mtm) cc_final: 0.6685 (mtp) REVERT: B 1770 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6012 (tm-30) REVERT: B 1962 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: B 2035 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7605 (mmp80) REVERT: B 2053 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7657 (tpt) REVERT: B 2119 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7356 (mp0) REVERT: B 2204 ASP cc_start: 0.6682 (t0) cc_final: 0.6316 (t0) outliers start: 49 outliers final: 13 residues processed: 219 average time/residue: 0.6479 time to fit residues: 158.9496 Evaluate side-chains 197 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1709 GLU Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2116 SER Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2190 HIS Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2230 LYS Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1770 GLU Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2124 VAL Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 152 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1642 GLN B1765 ASN B1943 HIS B2190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.228874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.174602 restraints weight = 26176.260| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.29 r_work: 0.3869 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18880 Z= 0.113 Angle : 0.551 10.097 25587 Z= 0.285 Chirality : 0.043 0.237 2831 Planarity : 0.004 0.043 3293 Dihedral : 7.235 77.652 2625 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 2.32 % Allowed : 13.65 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.62 (0.18), residues: 2271 helix: 1.36 (0.16), residues: 1038 sheet: 1.12 (0.26), residues: 387 loop : -1.12 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2212 TYR 0.014 0.001 TYR B2179 PHE 0.013 0.001 PHE A1666 TRP 0.020 0.001 TRP B2018 HIS 0.012 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00245 (18880) covalent geometry : angle 0.55133 (25587) hydrogen bonds : bond 0.03754 ( 917) hydrogen bonds : angle 4.41500 ( 2652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.729 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 988 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.4792 (tpt) REVERT: A 1021 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.3078 (tpt) REVERT: A 1076 LYS cc_start: 0.5424 (OUTLIER) cc_final: 0.5087 (tmtt) REVERT: A 1110 MET cc_start: 0.0884 (tmm) cc_final: -0.0573 (mpp) REVERT: A 1131 PHE cc_start: 0.5959 (m-80) cc_final: 0.5732 (m-80) REVERT: A 1253 MET cc_start: 0.2868 (pp-130) cc_final: 0.2321 (ptm) REVERT: A 1401 MET cc_start: 0.4643 (ppp) cc_final: 0.4297 (ppp) REVERT: A 1424 ARG cc_start: 0.5464 (mmt-90) cc_final: 0.5180 (mmt180) REVERT: A 1444 ASN cc_start: 0.5716 (m-40) cc_final: 0.5492 (m110) REVERT: A 1447 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6461 (mm-30) REVERT: A 1449 LEU cc_start: 0.7361 (mt) cc_final: 0.7098 (tm) REVERT: A 1510 GLN cc_start: 0.7335 (mt0) cc_final: 0.7042 (mp10) REVERT: A 1568 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6403 (tt) REVERT: A 1571 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6141 (mmm) REVERT: A 1742 GLU cc_start: 0.6435 (mp0) cc_final: 0.5340 (tp30) REVERT: A 1830 TYR cc_start: 0.8628 (m-80) cc_final: 0.8226 (m-80) REVERT: A 2000 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6472 (t0) REVERT: A 2197 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7198 (tp40) REVERT: A 2305 ARG cc_start: 0.5492 (mtm180) cc_final: 0.4926 (mtt180) REVERT: B 1630 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: B 1764 LEU cc_start: 0.8298 (mm) cc_final: 0.8075 (mp) REVERT: B 1770 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6233 (tm-30) REVERT: B 1926 VAL cc_start: 0.7734 (t) cc_final: 0.7533 (m) REVERT: B 1962 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 2035 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7673 (mmp80) REVERT: B 2053 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7683 (tpt) REVERT: B 2119 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7313 (mp0) REVERT: B 2204 ASP cc_start: 0.6726 (t0) cc_final: 0.6371 (t0) REVERT: B 2298 ASP cc_start: 0.7709 (t70) cc_final: 0.7368 (t0) REVERT: B 2301 LEU cc_start: 0.7264 (tp) cc_final: 0.7060 (pp) REVERT: B 2316 MET cc_start: 0.7297 (mmm) cc_final: 0.6906 (mmp) REVERT: B 2322 MET cc_start: 0.4625 (mtm) cc_final: 0.4169 (ptt) outliers start: 47 outliers final: 14 residues processed: 217 average time/residue: 0.6925 time to fit residues: 168.1487 Evaluate side-chains 201 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1571 MET Chi-restraints excluded: chain A residue 1616 MET Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2031 LYS Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2116 SER Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1770 GLU Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2093 TRP Chi-restraints excluded: chain B residue 2124 VAL Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2248 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN A1140 HIS ** A1287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1765 ASN ** B1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN B2190 HIS B2285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.220383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157084 restraints weight = 25582.266| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.83 r_work: 0.3695 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 18880 Z= 0.340 Angle : 0.791 10.567 25587 Z= 0.415 Chirality : 0.052 0.262 2831 Planarity : 0.007 0.110 3293 Dihedral : 8.106 81.996 2625 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.77 % Allowed : 13.80 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.10 (0.17), residues: 2271 helix: 0.69 (0.16), residues: 1024 sheet: 0.84 (0.25), residues: 390 loop : -1.41 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B2212 TYR 0.036 0.003 TYR B2081 PHE 0.037 0.003 PHE B1893 TRP 0.026 0.004 TRP B2018 HIS 0.012 0.002 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00801 (18880) covalent geometry : angle 0.79103 (25587) hydrogen bonds : bond 0.06042 ( 917) hydrogen bonds : angle 5.01267 ( 2652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4805 (tpt) REVERT: A 1021 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.3874 (mmp) REVERT: A 1076 LYS cc_start: 0.5538 (OUTLIER) cc_final: 0.5228 (tmtt) REVERT: A 1253 MET cc_start: 0.2908 (pp-130) cc_final: 0.2477 (ptm) REVERT: A 1290 ASN cc_start: 0.6805 (m-40) cc_final: 0.6214 (t0) REVERT: A 1401 MET cc_start: 0.4942 (ppp) cc_final: 0.4481 (ppp) REVERT: A 1447 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6812 (mm-30) REVERT: A 1586 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7574 (mttm) REVERT: A 1589 GLN cc_start: 0.7154 (tt0) cc_final: 0.6944 (tt0) REVERT: A 2000 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6528 (t0) REVERT: A 2137 MET cc_start: 0.8103 (mtt) cc_final: 0.7775 (mtt) REVERT: A 2162 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7200 (mmtm) REVERT: A 2190 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.6764 (p-80) REVERT: A 2197 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7148 (tp40) REVERT: A 2245 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7953 (mm110) REVERT: A 2305 ARG cc_start: 0.5535 (mtm180) cc_final: 0.5055 (mtt180) REVERT: A 2319 ILE cc_start: 0.5838 (mt) cc_final: 0.5584 (mm) REVERT: B 1604 MET cc_start: 0.7009 (mtm) cc_final: 0.6698 (mtp) REVERT: B 1616 MET cc_start: 0.6002 (mtt) cc_final: 0.5596 (mtt) REVERT: B 1630 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: B 1770 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: B 1774 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 2035 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7794 (mmp80) REVERT: B 2053 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8083 (tpt) REVERT: B 2119 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7544 (mp0) REVERT: B 2204 ASP cc_start: 0.6905 (t0) cc_final: 0.6704 (t0) REVERT: B 2298 ASP cc_start: 0.7885 (t70) cc_final: 0.7614 (t0) REVERT: B 2301 LEU cc_start: 0.7602 (tp) cc_final: 0.7375 (pp) REVERT: B 2316 MET cc_start: 0.7179 (mmm) cc_final: 0.6900 (mmp) outliers start: 56 outliers final: 23 residues processed: 227 average time/residue: 0.5754 time to fit residues: 147.5822 Evaluate side-chains 211 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1497 MET Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1586 LYS Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2190 HIS Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain A residue 2245 GLN Chi-restraints excluded: chain B residue 1592 SER Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1627 LEU Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1633 THR Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1770 GLU Chi-restraints excluded: chain B residue 1774 ASP Chi-restraints excluded: chain B residue 1909 SER Chi-restraints excluded: chain B residue 1943 HIS Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 2011 ILE Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2124 VAL Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2296 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 180 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1038 ASN B1765 ASN B1914 ASN B1943 HIS B2190 HIS B2234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.226286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.168256 restraints weight = 26060.076| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.08 r_work: 0.3815 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18880 Z= 0.125 Angle : 0.610 12.891 25587 Z= 0.313 Chirality : 0.044 0.387 2831 Planarity : 0.005 0.076 3293 Dihedral : 7.639 80.399 2625 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 2.08 % Allowed : 15.33 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.27 (0.18), residues: 2271 helix: 1.05 (0.16), residues: 1033 sheet: 0.95 (0.26), residues: 384 loop : -1.26 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2297 TYR 0.014 0.001 TYR A2299 PHE 0.014 0.001 PHE B1893 TRP 0.028 0.002 TRP B2018 HIS 0.016 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00276 (18880) covalent geometry : angle 0.61006 (25587) hydrogen bonds : bond 0.04134 ( 917) hydrogen bonds : angle 4.62356 ( 2652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3375 (tpt) REVERT: A 988 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.4742 (tpt) REVERT: A 1021 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.3865 (mmp) REVERT: A 1076 LYS cc_start: 0.5473 (OUTLIER) cc_final: 0.5205 (tmtt) REVERT: A 1110 MET cc_start: 0.1058 (tmm) cc_final: -0.0324 (mpp) REVERT: A 1253 MET cc_start: 0.3028 (pp-130) cc_final: 0.2580 (ptm) REVERT: A 1290 ASN cc_start: 0.6857 (m-40) cc_final: 0.6225 (t0) REVERT: A 1401 MET cc_start: 0.5025 (ppp) cc_final: 0.4603 (ppp) REVERT: A 1444 ASN cc_start: 0.5734 (m-40) cc_final: 0.5503 (m-40) REVERT: A 1489 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6668 (pt0) REVERT: A 1497 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7064 (tpp) REVERT: A 1571 MET cc_start: 0.7012 (mmm) cc_final: 0.6435 (tpt) REVERT: A 1760 ARG cc_start: 0.6465 (ptt90) cc_final: 0.6222 (ptt90) REVERT: A 1830 TYR cc_start: 0.8667 (m-80) cc_final: 0.8187 (m-80) REVERT: A 2000 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6400 (t0) REVERT: A 2138 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7067 (mmp-170) REVERT: A 2162 LYS cc_start: 0.7662 (mmpt) cc_final: 0.7326 (mmtm) REVERT: A 2190 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6756 (p-80) REVERT: A 2197 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.6991 (tp40) REVERT: A 2243 GLN cc_start: 0.8009 (mp10) cc_final: 0.7678 (mp-120) REVERT: A 2305 ARG cc_start: 0.5765 (mtm180) cc_final: 0.5163 (mtt180) REVERT: B 1604 MET cc_start: 0.6971 (mtm) cc_final: 0.6558 (mtp) REVERT: B 1630 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7836 (OUTLIER) REVERT: B 1770 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: B 1962 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: B 2035 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7624 (mmp80) REVERT: B 2053 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7662 (tpt) REVERT: B 2119 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7307 (mp0) REVERT: B 2204 ASP cc_start: 0.6975 (t0) cc_final: 0.6695 (t0) REVERT: B 2298 ASP cc_start: 0.7934 (t70) cc_final: 0.7548 (t0) REVERT: B 2305 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6918 (mtp-110) REVERT: B 2316 MET cc_start: 0.6867 (mmm) cc_final: 0.6597 (mmp) outliers start: 42 outliers final: 15 residues processed: 214 average time/residue: 0.5485 time to fit residues: 132.0484 Evaluate side-chains 202 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1497 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2138 ARG Chi-restraints excluded: chain A residue 2190 HIS Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1627 LEU Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1770 GLU Chi-restraints excluded: chain B residue 1943 HIS Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 1973 VAL Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2093 TRP Chi-restraints excluded: chain B residue 2124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1914 ASN B1943 HIS B2190 HIS B2234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.224069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162464 restraints weight = 25624.741| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.87 r_work: 0.3742 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18880 Z= 0.151 Angle : 0.630 13.095 25587 Z= 0.322 Chirality : 0.045 0.316 2831 Planarity : 0.005 0.071 3293 Dihedral : 7.567 79.758 2625 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 16.52 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.33 (0.18), residues: 2271 helix: 1.11 (0.16), residues: 1028 sheet: 0.94 (0.26), residues: 391 loop : -1.23 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1760 TYR 0.019 0.002 TYR A1404 PHE 0.024 0.002 PHE A1477 TRP 0.027 0.002 TRP A2018 HIS 0.015 0.001 HIS B1943 Details of bonding type rmsd covalent geometry : bond 0.00346 (18880) covalent geometry : angle 0.63000 (25587) hydrogen bonds : bond 0.04232 ( 917) hydrogen bonds : angle 4.59290 ( 2652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1021 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.3674 (mmp) REVERT: A 1076 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5259 (tmtt) REVERT: A 1110 MET cc_start: 0.0918 (tmm) cc_final: -0.0506 (mpp) REVERT: A 1253 MET cc_start: 0.3109 (pp-130) cc_final: 0.2755 (ptm) REVERT: A 1290 ASN cc_start: 0.6722 (m-40) cc_final: 0.6101 (t0) REVERT: A 1401 MET cc_start: 0.5041 (ppp) cc_final: 0.4609 (ppp) REVERT: A 1489 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6709 (pt0) REVERT: A 1497 MET cc_start: 0.7213 (tpt) cc_final: 0.7010 (tpp) REVERT: A 1568 LEU cc_start: 0.7027 (tp) cc_final: 0.6632 (tt) REVERT: A 1571 MET cc_start: 0.6774 (mmm) cc_final: 0.6381 (mmm) REVERT: A 1760 ARG cc_start: 0.6522 (ptt90) cc_final: 0.6281 (ptt90) REVERT: A 1830 TYR cc_start: 0.8672 (m-80) cc_final: 0.8247 (m-80) REVERT: A 2000 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6476 (t0) REVERT: A 2162 LYS cc_start: 0.7670 (mmpt) cc_final: 0.7347 (mmtm) REVERT: A 2197 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7112 (tp40) REVERT: A 2243 GLN cc_start: 0.8142 (mp10) cc_final: 0.7783 (mp-120) REVERT: A 2305 ARG cc_start: 0.5812 (mtm180) cc_final: 0.5241 (mtt180) REVERT: B 1604 MET cc_start: 0.6882 (mtm) cc_final: 0.6517 (mtp) REVERT: B 1630 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: B 1951 LEU cc_start: 0.7063 (mt) cc_final: 0.6792 (mp) REVERT: B 1962 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: B 2035 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7838 (mmp80) REVERT: B 2053 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7818 (tpt) REVERT: B 2119 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7419 (mp0) REVERT: B 2204 ASP cc_start: 0.6910 (t0) cc_final: 0.6663 (t0) REVERT: B 2305 ARG cc_start: 0.7283 (ttp80) cc_final: 0.7082 (mtp-110) REVERT: B 2316 MET cc_start: 0.6827 (mmm) cc_final: 0.6586 (mmp) outliers start: 30 outliers final: 13 residues processed: 199 average time/residue: 0.5744 time to fit residues: 128.9077 Evaluate side-chains 195 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2146 HIS Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1943 HIS Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 1973 VAL Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2093 TRP Chi-restraints excluded: chain B residue 2124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 0.4980 chunk 150 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1914 ASN B1943 HIS B2076 GLN B2104 HIS B2190 HIS B2234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.225226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165450 restraints weight = 25648.168| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.77 r_work: 0.3773 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18880 Z= 0.128 Angle : 0.611 12.380 25587 Z= 0.312 Chirality : 0.044 0.292 2831 Planarity : 0.004 0.066 3293 Dihedral : 7.435 79.213 2625 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.24 % Allowed : 17.06 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.18), residues: 2271 helix: 1.21 (0.16), residues: 1034 sheet: 0.98 (0.26), residues: 384 loop : -1.22 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1760 TYR 0.014 0.001 TYR B1830 PHE 0.021 0.001 PHE A1389 TRP 0.032 0.002 TRP A2018 HIS 0.011 0.001 HIS B2190 Details of bonding type rmsd covalent geometry : bond 0.00288 (18880) covalent geometry : angle 0.61073 (25587) hydrogen bonds : bond 0.03887 ( 917) hydrogen bonds : angle 4.50702 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.2472 (tpp) cc_final: 0.1829 (ppp) REVERT: A 886 MET cc_start: 0.3731 (tpt) cc_final: 0.3486 (tpt) REVERT: A 1021 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.3296 (mmp) REVERT: A 1076 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.5242 (tmtt) REVERT: A 1089 HIS cc_start: 0.5514 (t-170) cc_final: 0.4877 (m90) REVERT: A 1253 MET cc_start: 0.3115 (pp-130) cc_final: 0.2771 (ptm) REVERT: A 1290 ASN cc_start: 0.6741 (m-40) cc_final: 0.6096 (t0) REVERT: A 1401 MET cc_start: 0.5096 (ppp) cc_final: 0.4631 (ppp) REVERT: A 1489 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6732 (pt0) REVERT: A 1512 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 1568 LEU cc_start: 0.6990 (tp) cc_final: 0.6616 (tt) REVERT: A 1571 MET cc_start: 0.6637 (mmm) cc_final: 0.6358 (mmm) REVERT: A 1760 ARG cc_start: 0.6475 (ptt90) cc_final: 0.6216 (ptt90) REVERT: A 1830 TYR cc_start: 0.8624 (m-80) cc_final: 0.8200 (m-80) REVERT: A 2000 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6507 (t0) REVERT: A 2137 MET cc_start: 0.8160 (mmt) cc_final: 0.7788 (mmt) REVERT: A 2162 LYS cc_start: 0.7666 (mmpt) cc_final: 0.7348 (mmtm) REVERT: A 2197 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7028 (tp40) REVERT: A 2243 GLN cc_start: 0.8000 (mp10) cc_final: 0.7641 (mp-120) REVERT: A 2305 ARG cc_start: 0.5705 (mtm180) cc_final: 0.5077 (mtt-85) REVERT: B 1604 MET cc_start: 0.6796 (mtm) cc_final: 0.6513 (mtp) REVERT: B 1951 LEU cc_start: 0.7110 (mt) cc_final: 0.6785 (mp) REVERT: B 2035 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7798 (mmp80) REVERT: B 2053 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7684 (tpt) REVERT: B 2119 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7392 (mp0) REVERT: B 2204 ASP cc_start: 0.6816 (t0) cc_final: 0.6537 (t0) REVERT: B 2305 ARG cc_start: 0.7245 (ttp80) cc_final: 0.7035 (mtp-110) REVERT: B 2316 MET cc_start: 0.6831 (mmm) cc_final: 0.6594 (mmp) outliers start: 25 outliers final: 13 residues processed: 204 average time/residue: 0.5464 time to fit residues: 125.7386 Evaluate side-chains 194 residues out of total 2022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1076 LYS Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1688 ILE Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain A residue 2113 SER Chi-restraints excluded: chain A residue 2197 GLN Chi-restraints excluded: chain B residue 1610 ILE Chi-restraints excluded: chain B residue 1668 SER Chi-restraints excluded: chain B residue 1943 HIS Chi-restraints excluded: chain B residue 1952 SER Chi-restraints excluded: chain B residue 1962 GLU Chi-restraints excluded: chain B residue 1970 THR Chi-restraints excluded: chain B residue 1973 VAL Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2075 CYS Chi-restraints excluded: chain B residue 2093 TRP Chi-restraints excluded: chain B residue 2124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 146 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1534 ASN B1914 ASN B1943 HIS B2076 GLN ** B2190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2234 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.223586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.162720 restraints weight = 25563.161| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.09 r_work: 0.3749 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18880 Z= 0.184 Angle : 0.656 12.681 25587 Z= 0.336 Chirality : 0.046 0.302 2831 Planarity : 0.005 0.063 3293 Dihedral : 7.535 80.261 2625 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.34 % Allowed : 16.67 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.29 (0.18), residues: 2271 helix: 1.08 (0.16), residues: 1028 sheet: 0.91 (0.26), residues: 391 loop : -1.24 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B2212 TYR 0.023 0.002 TYR B1901 PHE 0.022 0.002 PHE B1893 TRP 0.035 0.002 TRP B2251 HIS 0.018 0.001 HIS B1943 Details of bonding type rmsd covalent geometry : bond 0.00431 (18880) covalent geometry : angle 0.65552 (25587) hydrogen bonds : bond 0.04482 ( 917) hydrogen bonds : angle 4.61942 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9915.89 seconds wall clock time: 168 minutes 31.99 seconds (10111.99 seconds total)