Starting phenix.real_space_refine on Mon Jul 6 15:57:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d30_46506/07_2026/9d30_46506.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 54 5.16 5 C 10987 2.51 5 N 3175 2.21 5 O 3368 1.98 5 H 17255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34840 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 18247 Classifications: {'peptide': 1215} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1157} Chain: "B" Number of atoms: 16567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 16567 Classifications: {'peptide': 1109} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1054} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'MU4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 5.40, per 1000 atoms: 0.15 Number of scatterers: 34840 At special positions: 0 Unit cell: (89.789, 108.458, 213.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 1 15.00 O 3368 8.00 N 3175 7.00 C 10987 6.00 H 17255 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 19 sheets defined 39.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 938 through 955 removed outlier: 3.649A pdb=" N TYR A 942 " --> pdb=" O PRO A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 removed outlier: 3.823A pdb=" N GLY A 999 " --> pdb=" O ASN A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1030 removed outlier: 3.825A pdb=" N GLN A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A1030 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1046 Processing helix chain 'A' and resid 1077 through 1086 removed outlier: 4.703A pdb=" N PHE A1082 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A1083 " --> pdb=" O ILE A1080 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1106 removed outlier: 4.284A pdb=" N VAL A1101 " --> pdb=" O CYS A1097 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A1103 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1188 Processing helix chain 'A' and resid 1223 through 1238 removed outlier: 4.312A pdb=" N ALA A1227 " --> pdb=" O PRO A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1267 removed outlier: 3.588A pdb=" N LYS A1264 " --> pdb=" O ALA A1260 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A1265 " --> pdb=" O GLY A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1310 removed outlier: 4.320A pdb=" N ALA A1293 " --> pdb=" O HIS A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1343 removed outlier: 3.716A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1355 removed outlier: 3.839A pdb=" N LEU A1347 " --> pdb=" O GLY A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 4.346A pdb=" N VAL A1374 " --> pdb=" O ASP A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1459 through 1467 Processing helix chain 'A' and resid 1522 through 1524 No H-bonds generated for 'chain 'A' and resid 1522 through 1524' Processing helix chain 'A' and resid 1532 through 1540 Processing helix chain 'A' and resid 1542 through 1552 removed outlier: 3.885A pdb=" N TYR A1548 " --> pdb=" O ALA A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1569 through 1583 Processing helix chain 'A' and resid 1592 through 1602 Processing helix chain 'A' and resid 1614 through 1622 Processing helix chain 'A' and resid 1637 through 1647 removed outlier: 4.057A pdb=" N ARG A1641 " --> pdb=" O GLY A1637 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1647 " --> pdb=" O GLY A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1664 removed outlier: 3.720A pdb=" N ASN A1664 " --> pdb=" O VAL A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1674 removed outlier: 3.734A pdb=" N ARG A1674 " --> pdb=" O PRO A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1690 Processing helix chain 'A' and resid 1690 through 1707 removed outlier: 3.525A pdb=" N VAL A1694 " --> pdb=" O GLN A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1733 removed outlier: 3.574A pdb=" N ALA A1726 " --> pdb=" O GLU A1722 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A1728 " --> pdb=" O ALA A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1788 removed outlier: 3.984A pdb=" N PHE A1779 " --> pdb=" O GLY A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1814 Processing helix chain 'A' and resid 1827 through 1841 Processing helix chain 'A' and resid 1864 through 1887 Proline residue: A1874 - end of helix removed outlier: 3.738A pdb=" N GLY A1878 " --> pdb=" O PRO A1874 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1904 Processing helix chain 'A' and resid 1910 through 1929 removed outlier: 3.551A pdb=" N ALA A1915 " --> pdb=" O ALA A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1944 through 1946 No H-bonds generated for 'chain 'A' and resid 1944 through 1946' Processing helix chain 'A' and resid 1947 through 1952 Processing helix chain 'A' and resid 1959 through 1971 removed outlier: 3.636A pdb=" N TYR A1965 " --> pdb=" O GLU A1961 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1966 " --> pdb=" O GLU A1962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 1996 removed outlier: 3.984A pdb=" N ARG A1994 " --> pdb=" O ALA A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2013 Processing helix chain 'A' and resid 2014 through 2019 removed outlier: 3.504A pdb=" N GLU A2018 " --> pdb=" O LYS A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2022 No H-bonds generated for 'chain 'A' and resid 2020 through 2022' Processing helix chain 'A' and resid 2023 through 2044 removed outlier: 3.953A pdb=" N ARG A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A2041 " --> pdb=" O GLU A2037 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A2042 " --> pdb=" O GLN A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2057 removed outlier: 4.164A pdb=" N TYR A2056 " --> pdb=" O SER A2052 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A2057 " --> pdb=" O PHE A2053 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2052 through 2057' Processing helix chain 'A' and resid 2061 through 2075 Processing helix chain 'A' and resid 2081 through 2086 removed outlier: 3.594A pdb=" N THR A2085 " --> pdb=" O LYS A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2106 removed outlier: 4.065A pdb=" N GLU A2103 " --> pdb=" O THR A2099 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 930 through 934 Processing helix chain 'B' and resid 938 through 954 removed outlier: 4.157A pdb=" N TYR B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS B 943 " --> pdb=" O GLY B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1000 removed outlier: 3.534A pdb=" N GLY B 999 " --> pdb=" O ASN B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 4.106A pdb=" N ALA B1033 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B1034 " --> pdb=" O PRO B1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1030 through 1034' Processing helix chain 'B' and resid 1035 through 1036 No H-bonds generated for 'chain 'B' and resid 1035 through 1036' Processing helix chain 'B' and resid 1037 through 1042 Processing helix chain 'B' and resid 1042 through 1047 removed outlier: 4.087A pdb=" N ARG B1046 " --> pdb=" O SER B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1082 Processing helix chain 'B' and resid 1090 through 1106 removed outlier: 3.872A pdb=" N LEU B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B1101 " --> pdb=" O CYS B1097 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1190 removed outlier: 3.772A pdb=" N ARG B1184 " --> pdb=" O ASP B1180 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B1185 " --> pdb=" O GLU B1181 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B1188 " --> pdb=" O ARG B1184 " (cutoff:3.500A) Processing helix chain 'B' and resid 1222 through 1238 removed outlier: 3.898A pdb=" N LEU B1226 " --> pdb=" O THR B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1254 through 1259 Processing helix chain 'B' and resid 1287 through 1311 removed outlier: 3.719A pdb=" N LEU B1291 " --> pdb=" O ASP B1287 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B1292 " --> pdb=" O GLU B1288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B1299 " --> pdb=" O ARG B1295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B1311 " --> pdb=" O GLU B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1339 through 1342 Processing helix chain 'B' and resid 1343 through 1355 removed outlier: 4.035A pdb=" N LEU B1347 " --> pdb=" O GLY B1343 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1380 Processing helix chain 'B' and resid 1405 through 1409 removed outlier: 3.644A pdb=" N GLU B1408 " --> pdb=" O GLY B1405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B1409 " --> pdb=" O HIS B1406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1405 through 1409' Processing helix chain 'B' and resid 1459 through 1467 Processing helix chain 'B' and resid 1520 through 1522 No H-bonds generated for 'chain 'B' and resid 1520 through 1522' Processing helix chain 'B' and resid 1532 through 1540 Processing helix chain 'B' and resid 1542 through 1551 removed outlier: 3.827A pdb=" N TYR B1548 " --> pdb=" O ALA B1544 " (cutoff:3.500A) Processing helix chain 'B' and resid 1569 through 1582 Processing helix chain 'B' and resid 1592 through 1603 Processing helix chain 'B' and resid 1614 through 1623 Processing helix chain 'B' and resid 1636 through 1647 removed outlier: 3.728A pdb=" N GLN B1640 " --> pdb=" O THR B1636 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B1641 " --> pdb=" O GLY B1637 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B1647 " --> pdb=" O GLY B1643 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1663 removed outlier: 4.315A pdb=" N VAL B1661 " --> pdb=" O GLY B1657 " (cutoff:3.500A) Processing helix chain 'B' and resid 1670 through 1675 removed outlier: 3.548A pdb=" N ARG B1674 " --> pdb=" O PRO B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1682 through 1690 Processing helix chain 'B' and resid 1690 through 1707 removed outlier: 3.507A pdb=" N VAL B1694 " --> pdb=" O GLN B1690 " (cutoff:3.500A) Processing helix chain 'B' and resid 1722 through 1732 removed outlier: 3.581A pdb=" N ALA B1726 " --> pdb=" O GLU B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1774 through 1787 Processing helix chain 'B' and resid 1801 through 1814 removed outlier: 3.746A pdb=" N THR B1807 " --> pdb=" O LYS B1803 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B1808 " --> pdb=" O ALA B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1827 through 1841 Processing helix chain 'B' and resid 1859 through 1864 removed outlier: 5.750A pdb=" N THR B1864 " --> pdb=" O THR B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1865 through 1876 removed outlier: 4.216A pdb=" N ASP B1869 " --> pdb=" O ASP B1865 " (cutoff:3.500A) Proline residue: B1874 - end of helix Processing helix chain 'B' and resid 1876 through 1885 Processing helix chain 'B' and resid 1900 through 1905 Processing helix chain 'B' and resid 1910 through 1930 removed outlier: 3.819A pdb=" N ALA B1914 " --> pdb=" O GLY B1910 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B1918 " --> pdb=" O ALA B1914 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B1919 " --> pdb=" O ALA B1915 " (cutoff:3.500A) Processing helix chain 'B' and resid 1961 through 1972 Processing helix chain 'B' and resid 1986 through 1996 removed outlier: 4.151A pdb=" N ALA B1990 " --> pdb=" O ALA B1986 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B1991 " --> pdb=" O PRO B1987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 901 through 904 removed outlier: 3.681A pdb=" N GLU A 910 " --> pdb=" O ILE A 983 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 984 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A1005 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS A1004 " --> pdb=" O PHE A 965 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE A 965 " --> pdb=" O HIS A1004 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A1006 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE A 963 " --> pdb=" O THR A1006 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 901 through 904 Processing sheet with id=AA3, first strand: chain 'A' and resid 1117 through 1125 removed outlier: 3.794A pdb=" N ARG A1171 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A1120 " --> pdb=" O GLY A1169 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY A1169 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER A1122 " --> pdb=" O VAL A1167 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL A1167 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A1124 " --> pdb=" O LEU A1165 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A1165 " --> pdb=" O ARG A1124 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A1156 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A1155 " --> pdb=" O TYR A1136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1212 through 1215 removed outlier: 6.586A pdb=" N LEU A1212 " --> pdb=" O VAL A1276 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A1278 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A1214 " --> pdb=" O VAL A1278 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A1275 " --> pdb=" O PHE A1319 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A1321 " --> pdb=" O VAL A1275 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A1277 " --> pdb=" O VAL A1321 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ARG A1323 " --> pdb=" O ILE A1277 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A1363 " --> pdb=" O LEU A1318 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL A1320 " --> pdb=" O ILE A1363 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A1365 " --> pdb=" O VAL A1320 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR A1322 " --> pdb=" O VAL A1365 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1362 " --> pdb=" O THR A1387 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N TRP A1389 " --> pdb=" O LEU A1362 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A1364 " --> pdb=" O TRP A1389 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU A1386 " --> pdb=" O ALA A1397 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TRP A1394 " --> pdb=" O ARG A1198 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A1193 " --> pdb=" O TYR A1977 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N TYR A1977 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A1896 " --> pdb=" O ILE A1936 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP A1938 " --> pdb=" O LEU A1896 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A1898 " --> pdb=" O TRP A1938 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A1895 " --> pdb=" O VAL A1848 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER A1766 " --> pdb=" O LEU A1845 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A1847 " --> pdb=" O SER A1766 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR A1767 " --> pdb=" O VAL A1793 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR A1795 " --> pdb=" O TYR A1767 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A1769 " --> pdb=" O THR A1795 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1796 " --> pdb=" O GLU A1821 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1411 through 1414 Processing sheet with id=AA6, first strand: chain 'A' and resid 1421 through 1425 removed outlier: 3.827A pdb=" N GLN A1424 " --> pdb=" O GLU A1435 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A1435 " --> pdb=" O GLN A1424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1503 through 1507 removed outlier: 7.454A pdb=" N ASP A1483 " --> pdb=" O SER A1456 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A1456 " --> pdb=" O ASP A1483 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A1485 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A1450 " --> pdb=" O THR A1489 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL A1491 " --> pdb=" O GLN A1448 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A1448 " --> pdb=" O VAL A1491 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A1519 " --> pdb=" O ILE A1449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1503 through 1507 removed outlier: 7.454A pdb=" N ASP A1483 " --> pdb=" O SER A1456 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER A1456 " --> pdb=" O ASP A1483 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A1485 " --> pdb=" O SER A1454 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A1450 " --> pdb=" O THR A1489 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL A1491 " --> pdb=" O GLN A1448 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN A1448 " --> pdb=" O VAL A1491 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR A1718 " --> pdb=" O ASP A1742 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1562 through 1564 removed outlier: 7.607A pdb=" N LEU A1563 " --> pdb=" O LEU A1632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1588 through 1590 Processing sheet with id=AB2, first strand: chain 'A' and resid 1653 through 1655 removed outlier: 6.384A pdb=" N PHE A1653 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE B1653 " --> pdb=" O TYR B1679 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS B1561 " --> pdb=" O ILE B1630 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B1632 " --> pdb=" O LYS B1561 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B1563 " --> pdb=" O LEU B1632 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N TYR B1608 " --> pdb=" O ILE B1586 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA B1588 " --> pdb=" O TYR B1608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 903 through 905 Processing sheet with id=AB4, first strand: chain 'B' and resid 903 through 905 removed outlier: 3.515A pdb=" N ASP B 984 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B 988 " --> pdb=" O ASP B 984 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 989 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B1005 " --> pdb=" O VAL B 993 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B1008 " --> pdb=" O ASP B 962 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP B 962 " --> pdb=" O ALA B1008 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG B1010 " --> pdb=" O VAL B 960 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL B 960 " --> pdb=" O ARG B1010 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA B 958 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B1125 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG B1121 " --> pdb=" O ASP B 962 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR B 964 " --> pdb=" O GLY B1119 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B1119 " --> pdb=" O THR B 964 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B1169 " --> pdb=" O ARG B1121 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B1123 " --> pdb=" O VAL B1167 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL B1167 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B1125 " --> pdb=" O LEU B1165 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B1165 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B1156 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA B1166 " --> pdb=" O LEU B1154 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B1154 " --> pdb=" O ALA B1166 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ARG B1168 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA B1152 " --> pdb=" O ARG B1168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1191 through 1197 removed outlier: 3.541A pdb=" N THR B1192 " --> pdb=" O THR B1400 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU B1386 " --> pdb=" O ALA B1397 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B1362 " --> pdb=" O THR B1387 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TRP B1389 " --> pdb=" O LEU B1362 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP B1364 " --> pdb=" O TRP B1389 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B1318 " --> pdb=" O THR B1361 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B1363 " --> pdb=" O LEU B1318 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B1320 " --> pdb=" O ILE B1363 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B1365 " --> pdb=" O VAL B1320 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B1322 " --> pdb=" O VAL B1365 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B1212 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B1278 " --> pdb=" O LEU B1212 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B1214 " --> pdb=" O VAL B1278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1411 through 1414 removed outlier: 3.685A pdb=" N ALA B1412 " --> pdb=" O ALA B1752 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1421 through 1425 Processing sheet with id=AB8, first strand: chain 'B' and resid 1524 through 1526 removed outlier: 7.609A pdb=" N ASP B1483 " --> pdb=" O SER B1456 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER B1456 " --> pdb=" O ASP B1483 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B1485 " --> pdb=" O SER B1454 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B1487 " --> pdb=" O ALA B1452 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU B1450 " --> pdb=" O THR B1489 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR B1716 " --> pdb=" O VAL B1740 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP B1742 " --> pdb=" O THR B1716 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B1718 " --> pdb=" O ASP B1742 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1792 through 1795 removed outlier: 7.805A pdb=" N TYR B1767 " --> pdb=" O VAL B1793 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR B1795 " --> pdb=" O TYR B1767 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B1769 " --> pdb=" O THR B1795 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER B1766 " --> pdb=" O ARG B1846 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B1848 " --> pdb=" O SER B1766 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B1768 " --> pdb=" O VAL B1848 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N HIS B1850 " --> pdb=" O ILE B1768 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1770 " --> pdb=" O HIS B1850 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B1893 " --> pdb=" O ARG B1846 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B1848 " --> pdb=" O TRP B1893 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1897 through 1898 removed outlier: 3.587A pdb=" N SER B1978 " --> pdb=" O ALA B1935 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1893 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: 9.14 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17233 1.03 - 1.23: 34 1.23 - 1.42: 7481 1.42 - 1.62: 10359 1.62 - 1.81: 87 Bond restraints: 35194 Sorted by residual: bond pdb=" O27 MU4 A2201 " pdb=" P24 MU4 A2201 " ideal model delta sigma weight residual 1.718 1.620 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N VAL A1186 " pdb=" CA VAL A1186 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.23e-02 6.61e+03 1.67e+01 bond pdb=" N VAL A 931 " pdb=" CA VAL A 931 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.08e-02 8.57e+03 1.19e+01 bond pdb=" CA SER A 927 " pdb=" CB SER A 927 " ideal model delta sigma weight residual 1.524 1.487 0.038 1.22e-02 6.72e+03 9.62e+00 bond pdb=" N THR A 964 " pdb=" CA THR A 964 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.25e-02 6.40e+03 8.05e+00 ... (remaining 35189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 62954 1.97 - 3.94: 471 3.94 - 5.91: 49 5.91 - 7.88: 6 7.88 - 9.85: 3 Bond angle restraints: 63483 Sorted by residual: angle pdb=" N LEU A2061 " pdb=" CA LEU A2061 " pdb=" C LEU A2061 " ideal model delta sigma weight residual 113.55 103.70 9.85 1.26e+00 6.30e-01 6.11e+01 angle pdb=" CA PRO B1960 " pdb=" N PRO B1960 " pdb=" CD PRO B1960 " ideal model delta sigma weight residual 112.00 102.52 9.48 1.40e+00 5.10e-01 4.59e+01 angle pdb=" N GLY A2062 " pdb=" CA GLY A2062 " pdb=" C GLY A2062 " ideal model delta sigma weight residual 113.37 104.92 8.45 1.34e+00 5.57e-01 3.98e+01 angle pdb=" N SER A2060 " pdb=" CA SER A2060 " pdb=" C SER A2060 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.17e+00 7.31e-01 3.78e+01 angle pdb=" N LEU A 926 " pdb=" CA LEU A 926 " pdb=" C LEU A 926 " ideal model delta sigma weight residual 111.33 104.81 6.52 1.21e+00 6.83e-01 2.90e+01 ... (remaining 63478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 15738 33.74 - 67.48: 730 67.48 - 101.22: 60 101.22 - 134.97: 0 134.97 - 168.71: 2 Dihedral angle restraints: 16530 sinusoidal: 9066 harmonic: 7464 Sorted by residual: dihedral pdb=" C2 MU4 A2201 " pdb=" C3 MU4 A2201 " pdb=" C4 MU4 A2201 " pdb=" C5 MU4 A2201 " ideal model delta sinusoidal sigma weight residual 168.61 -22.68 -168.71 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 MU4 A2201 " pdb=" C42 MU4 A2201 " pdb=" C43 MU4 A2201 " pdb=" N41 MU4 A2201 " ideal model delta sinusoidal sigma weight residual 306.78 157.00 149.78 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" CA GLY A1651 " pdb=" C GLY A1651 " pdb=" N ARG A1652 " pdb=" CA ARG A1652 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1873 0.032 - 0.063: 586 0.063 - 0.095: 167 0.095 - 0.127: 130 0.127 - 0.158: 11 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CA MET A 968 " pdb=" N MET A 968 " pdb=" C MET A 968 " pdb=" CB MET A 968 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA PHE A 965 " pdb=" N PHE A 965 " pdb=" C PHE A 965 " pdb=" CB PHE A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA LEU A2058 " pdb=" N LEU A2058 " pdb=" C LEU A2058 " pdb=" CB LEU A2058 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 2764 not shown) Planarity restraints: 5455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1189 " -0.710 9.50e-02 1.11e+02 5.02e-01 4.46e+03 pdb=" NE ARG A1189 " -0.256 2.00e-02 2.50e+03 pdb=" CZ ARG A1189 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A1189 " 0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG A1189 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A1189 " -0.646 2.00e-02 2.50e+03 pdb="HH12 ARG A1189 " 0.867 2.00e-02 2.50e+03 pdb="HH21 ARG A1189 " 0.535 2.00e-02 2.50e+03 pdb="HH22 ARG A1189 " -0.484 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2045 " 1.106 9.50e-02 1.11e+02 5.03e-01 2.77e+03 pdb=" NE ARG A2045 " 0.381 2.00e-02 2.50e+03 pdb=" CZ ARG A2045 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG A2045 " -0.060 2.00e-02 2.50e+03 pdb=" NH2 ARG A2045 " -0.050 2.00e-02 2.50e+03 pdb="HH11 ARG A2045 " -0.619 2.00e-02 2.50e+03 pdb="HH12 ARG A2045 " 0.408 2.00e-02 2.50e+03 pdb="HH21 ARG A2045 " -0.500 2.00e-02 2.50e+03 pdb="HH22 ARG A2045 " 0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 930 " -0.254 2.00e-02 2.50e+03 3.37e-01 1.70e+03 pdb=" CD GLN A 930 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN A 930 " 0.247 2.00e-02 2.50e+03 pdb=" NE2 GLN A 930 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 930 " 0.521 2.00e-02 2.50e+03 pdb="HE22 GLN A 930 " -0.532 2.00e-02 2.50e+03 ... (remaining 5452 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 1150 2.11 - 2.73: 62539 2.73 - 3.35: 102811 3.35 - 3.98: 126732 3.98 - 4.60: 197441 Nonbonded interactions: 490673 Sorted by model distance: nonbonded pdb=" O GLU A1202 " pdb=" H GLY A1204 " model vdw 1.487 2.450 nonbonded pdb=" OD1 ASP A1764 " pdb="HH22 ARG A1846 " model vdw 1.531 2.450 nonbonded pdb=" O HIS A1061 " pdb=" H LEU A1071 " model vdw 1.545 2.450 nonbonded pdb=" O PHE A1098 " pdb=" H VAL A1101 " model vdw 1.558 2.450 nonbonded pdb=" H ASP A 962 " pdb=" O ARG A1121 " model vdw 1.563 2.450 ... (remaining 490668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 892 through 1849 or (resid 1850 and (name N or name CA or \ name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or na \ me NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or n \ ame HE2)) or resid 1851 through 2000)) selection = (chain 'B' and (resid 892 through 911 or (resid 912 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 913 through 928 or (resid 929 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 930 through 1330 or (resid 1331 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 133 \ 2 through 2000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.220 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 33.350 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.748 17942 Z= 0.592 Angle : 0.604 9.853 24426 Z= 0.344 Chirality : 0.040 0.158 2767 Planarity : 0.008 0.232 3244 Dihedral : 16.216 168.708 6453 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.97 % Favored : 90.69 % Rotamer: Outliers : 0.72 % Allowed : 19.99 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2320 helix: 0.63 (0.20), residues: 782 sheet: -1.28 (0.27), residues: 363 loop : -2.13 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2045 TYR 0.011 0.001 TYR A1087 PHE 0.026 0.001 PHE B1649 TRP 0.012 0.001 TRP A1998 HIS 0.006 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (17939) covalent geometry : angle 0.60429 / 0.34 (24426) hydrogen bonds : bond 0.19973 / 13.71 ( 650) hydrogen bonds : angle 7.75617 / 5.60 ( 1893) Misc. bond : bond 0.43552 / 20.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 490 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 477 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 969 LEU cc_start: 0.8994 (mt) cc_final: 0.8685 (mp) REVERT: A 970 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 994 GLU cc_start: 0.8743 (pt0) cc_final: 0.8210 (pt0) REVERT: A 1131 ASN cc_start: 0.8698 (p0) cc_final: 0.8396 (p0) REVERT: A 1630 ILE cc_start: 0.9363 (mp) cc_final: 0.8933 (mp) REVERT: A 1780 PHE cc_start: 0.9343 (m-80) cc_final: 0.9112 (m-80) REVERT: A 1882 LEU cc_start: 0.9747 (mt) cc_final: 0.9535 (mt) REVERT: A 1921 VAL cc_start: 0.9521 (t) cc_final: 0.9098 (p) REVERT: A 2016 ARG cc_start: 0.8966 (mmm160) cc_final: 0.8398 (tpt170) REVERT: A 2081 LYS cc_start: 0.9607 (tppp) cc_final: 0.9370 (tppp) REVERT: B 944 GLU cc_start: 0.9144 (tp30) cc_final: 0.8464 (tm-30) REVERT: B 967 GLN cc_start: 0.9365 (pt0) cc_final: 0.9019 (pp30) REVERT: B 1040 ARG cc_start: 0.8835 (mpt180) cc_final: 0.8441 (mtm-85) REVERT: B 1189 ARG cc_start: 0.9295 (mmt90) cc_final: 0.8872 (mmt90) REVERT: B 1981 ILE cc_start: 0.9045 (pt) cc_final: 0.8804 (pt) outliers start: 13 outliers final: 8 residues processed: 481 average time/residue: 0.3255 time to fit residues: 234.0385 Evaluate side-chains 398 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 389 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2060 SER Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1218 ASN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN B1252 GLN B1368 HIS B1640 GLN B1909 GLN B1929 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059409 restraints weight = 166473.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062952 restraints weight = 73404.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065403 restraints weight = 44378.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067038 restraints weight = 31784.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068122 restraints weight = 25399.920| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17942 Z= 0.209 Angle : 0.620 6.477 24426 Z= 0.333 Chirality : 0.041 0.139 2767 Planarity : 0.005 0.097 3244 Dihedral : 7.298 175.377 2572 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.05 % Favored : 90.73 % Rotamer: Outliers : 2.06 % Allowed : 23.16 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.17), residues: 2320 helix: 0.34 (0.18), residues: 797 sheet: -1.35 (0.27), residues: 369 loop : -2.35 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1124 TYR 0.019 0.002 TYR A1087 PHE 0.009 0.001 PHE B1967 TRP 0.014 0.001 TRP A1998 HIS 0.010 0.001 HIS B1368 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (17939) covalent geometry : angle 0.61978 / 0.33 (24426) hydrogen bonds : bond 0.05578 / 3.85 ( 650) hydrogen bonds : angle 6.37122 / 4.54 ( 1893) Misc. bond : bond 0.00328 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 389 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 HIS cc_start: 0.8466 (m90) cc_final: 0.7771 (m-70) REVERT: A 969 LEU cc_start: 0.9292 (mt) cc_final: 0.8926 (mp) REVERT: A 970 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 972 ASP cc_start: 0.8488 (m-30) cc_final: 0.8073 (m-30) REVERT: A 975 THR cc_start: 0.9385 (m) cc_final: 0.9184 (p) REVERT: A 994 GLU cc_start: 0.8879 (pt0) cc_final: 0.8351 (pt0) REVERT: A 1200 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 1377 GLN cc_start: 0.9623 (tp40) cc_final: 0.9422 (tt0) REVERT: A 1421 MET cc_start: 0.9124 (pmm) cc_final: 0.8402 (pmm) REVERT: A 1586 ILE cc_start: 0.9129 (mp) cc_final: 0.8778 (mt) REVERT: A 2016 ARG cc_start: 0.9210 (mmm160) cc_final: 0.8305 (tpt170) REVERT: A 2038 GLN cc_start: 0.8953 (mt0) cc_final: 0.8545 (mt0) REVERT: A 2065 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9034 (mm-30) REVERT: A 2073 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8625 (mp0) REVERT: A 2081 LYS cc_start: 0.9665 (tppp) cc_final: 0.9452 (tppp) REVERT: B 972 ASP cc_start: 0.7965 (p0) cc_final: 0.7578 (p0) outliers start: 37 outliers final: 27 residues processed: 409 average time/residue: 0.2935 time to fit residues: 185.7782 Evaluate side-chains 387 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 943 CYS Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1187 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1211 TRP Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1808 ILE Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1564 ILE Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1633 ASN Chi-restraints excluded: chain B residue 1640 GLN Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1784 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 138 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1424 GLN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 HIS B1640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058569 restraints weight = 165691.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061942 restraints weight = 73667.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064272 restraints weight = 44569.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065788 restraints weight = 31805.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066926 restraints weight = 25399.198| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17942 Z= 0.224 Angle : 0.603 8.245 24426 Z= 0.322 Chirality : 0.040 0.168 2767 Planarity : 0.004 0.072 3244 Dihedral : 6.936 172.714 2564 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.74 % Favored : 90.09 % Rotamer: Outliers : 3.12 % Allowed : 21.66 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.17), residues: 2320 helix: 0.17 (0.18), residues: 798 sheet: -1.51 (0.26), residues: 378 loop : -2.43 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1926 TYR 0.016 0.002 TYR B1680 PHE 0.009 0.001 PHE A1780 TRP 0.015 0.001 TRP A1998 HIS 0.007 0.001 HIS B1924 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (17939) covalent geometry : angle 0.60315 / 0.32 (24426) hydrogen bonds : bond 0.04673 / 3.20 ( 650) hydrogen bonds : angle 5.99417 / 4.27 ( 1893) Misc. bond : bond 0.00400 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 359 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 969 LEU cc_start: 0.9328 (mt) cc_final: 0.9001 (mp) REVERT: A 970 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8061 (pp) REVERT: A 972 ASP cc_start: 0.8511 (m-30) cc_final: 0.8126 (m-30) REVERT: A 975 THR cc_start: 0.9392 (m) cc_final: 0.9191 (p) REVERT: A 994 GLU cc_start: 0.8837 (pt0) cc_final: 0.8331 (pt0) REVERT: A 1200 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7955 (mt) REVERT: A 1273 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.7159 (t0) REVERT: A 1424 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8373 (pp30) REVERT: A 1586 ILE cc_start: 0.9157 (mp) cc_final: 0.8821 (mt) REVERT: A 1655 GLU cc_start: 0.8305 (tp30) cc_final: 0.7898 (tp30) REVERT: A 2016 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8270 (tpt170) REVERT: A 2065 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9146 (mm-30) REVERT: A 2081 LYS cc_start: 0.9675 (tppp) cc_final: 0.9458 (tppp) REVERT: B 1640 GLN cc_start: 0.9605 (OUTLIER) cc_final: 0.9182 (pp30) REVERT: B 1994 ARG cc_start: 0.9052 (mtm180) cc_final: 0.8792 (tpp80) outliers start: 56 outliers final: 42 residues processed: 393 average time/residue: 0.3031 time to fit residues: 185.0603 Evaluate side-chains 385 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1211 TRP Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1808 ILE Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1502 ASP Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1640 GLN Chi-restraints excluded: chain B residue 1681 LEU Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1768 ILE Chi-restraints excluded: chain B residue 1769 ILE Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 24 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 157 optimal weight: 0.0970 chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 0.0040 chunk 216 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059585 restraints weight = 166540.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063134 restraints weight = 73252.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065576 restraints weight = 44151.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067207 restraints weight = 31537.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068297 restraints weight = 25144.139| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17942 Z= 0.128 Angle : 0.582 12.713 24426 Z= 0.302 Chirality : 0.040 0.155 2767 Planarity : 0.004 0.062 3244 Dihedral : 6.791 171.573 2564 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 2.28 % Allowed : 22.66 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2320 helix: 0.43 (0.19), residues: 792 sheet: -1.40 (0.27), residues: 369 loop : -2.32 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1926 TYR 0.033 0.002 TYR B1980 PHE 0.007 0.001 PHE A 965 TRP 0.013 0.001 TRP A1998 HIS 0.007 0.001 HIS B1924 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17939) covalent geometry : angle 0.58162 / 0.30 (24426) hydrogen bonds : bond 0.04069 / 2.76 ( 650) hydrogen bonds : angle 5.65483 / 4.02 ( 1893) Misc. bond : bond 0.00119 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 360 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9737 (tp) cc_final: 0.9485 (tp) REVERT: A 969 LEU cc_start: 0.9341 (mt) cc_final: 0.8986 (mp) REVERT: A 970 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8077 (pp) REVERT: A 972 ASP cc_start: 0.8467 (m-30) cc_final: 0.8122 (m-30) REVERT: A 994 GLU cc_start: 0.8823 (pt0) cc_final: 0.8358 (pt0) REVERT: A 1225 MET cc_start: 0.8840 (pmm) cc_final: 0.8533 (pmm) REVERT: A 1424 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8524 (pp30) REVERT: A 1586 ILE cc_start: 0.9182 (mp) cc_final: 0.8893 (mt) REVERT: A 1655 GLU cc_start: 0.8269 (tp30) cc_final: 0.7868 (tp30) REVERT: A 1656 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9019 (pt) REVERT: A 1845 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 1977 TYR cc_start: 0.8545 (t80) cc_final: 0.8279 (t80) REVERT: A 1991 ASP cc_start: 0.9221 (t0) cc_final: 0.8892 (m-30) REVERT: A 2016 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8280 (tpt170) REVERT: A 2065 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9152 (mm-30) REVERT: A 2081 LYS cc_start: 0.9665 (tppp) cc_final: 0.9437 (tppp) REVERT: B 1482 MET cc_start: 0.9078 (ttp) cc_final: 0.8241 (ptm) REVERT: B 1614 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9107 (mt-10) REVERT: B 1994 ARG cc_start: 0.9028 (mtm180) cc_final: 0.8767 (tpp80) outliers start: 41 outliers final: 36 residues processed: 382 average time/residue: 0.3047 time to fit residues: 181.6254 Evaluate side-chains 383 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1211 TRP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1983 ILE Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1301 LEU Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 113 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.089593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057923 restraints weight = 168243.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061371 restraints weight = 74616.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063778 restraints weight = 45329.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065388 restraints weight = 32512.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066490 restraints weight = 25947.816| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17942 Z= 0.209 Angle : 0.593 6.499 24426 Z= 0.313 Chirality : 0.040 0.157 2767 Planarity : 0.004 0.051 3244 Dihedral : 6.748 170.217 2564 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.91 % Favored : 89.87 % Rotamer: Outliers : 3.45 % Allowed : 22.77 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2320 helix: 0.31 (0.18), residues: 792 sheet: -1.49 (0.27), residues: 374 loop : -2.39 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1441 TYR 0.036 0.002 TYR B1980 PHE 0.021 0.001 PHE A2002 TRP 0.013 0.001 TRP A1998 HIS 0.007 0.001 HIS B1924 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (17939) covalent geometry : angle 0.59344 / 0.31 (24426) hydrogen bonds : bond 0.03917 / 2.66 ( 650) hydrogen bonds : angle 5.61366 / 4.00 ( 1893) Misc. bond : bond 0.00113 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 341 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 969 LEU cc_start: 0.9345 (mt) cc_final: 0.9050 (mp) REVERT: A 970 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 972 ASP cc_start: 0.8485 (m-30) cc_final: 0.8179 (m-30) REVERT: A 994 GLU cc_start: 0.8772 (pt0) cc_final: 0.8329 (pt0) REVERT: A 1039 MET cc_start: 0.9192 (tpt) cc_final: 0.8909 (tmm) REVERT: A 1211 TRP cc_start: 0.8413 (OUTLIER) cc_final: 0.7649 (m100) REVERT: A 1225 MET cc_start: 0.8873 (pmm) cc_final: 0.8540 (pmm) REVERT: A 1273 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.7243 (t70) REVERT: A 1424 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: A 1586 ILE cc_start: 0.9160 (mp) cc_final: 0.8647 (mt) REVERT: A 1655 GLU cc_start: 0.8278 (tp30) cc_final: 0.7876 (tp30) REVERT: A 1845 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 1865 ASP cc_start: 0.9442 (OUTLIER) cc_final: 0.9186 (m-30) REVERT: A 1991 ASP cc_start: 0.9278 (t0) cc_final: 0.8953 (m-30) REVERT: A 2017 MET cc_start: 0.8970 (ttt) cc_final: 0.8654 (ttt) REVERT: A 2065 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9187 (mm-30) REVERT: A 2081 LYS cc_start: 0.9673 (tppp) cc_final: 0.9441 (tppp) REVERT: B 1617 GLU cc_start: 0.9325 (tt0) cc_final: 0.9064 (tm-30) REVERT: B 1994 ARG cc_start: 0.9054 (mtm180) cc_final: 0.8789 (tpp80) outliers start: 62 outliers final: 46 residues processed: 379 average time/residue: 0.3056 time to fit residues: 179.2233 Evaluate side-chains 381 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1211 TRP Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1879 SER Chi-restraints excluded: chain A residue 1924 HIS Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1502 ASP Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1586 ILE Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1769 ILE Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1926 ARG Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 193 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 217 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** A1924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1300 HIS B1640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059290 restraints weight = 164280.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062848 restraints weight = 72467.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065305 restraints weight = 43834.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066975 restraints weight = 31332.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.068038 restraints weight = 24946.382| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17942 Z= 0.119 Angle : 0.583 9.139 24426 Z= 0.299 Chirality : 0.041 0.168 2767 Planarity : 0.004 0.133 3244 Dihedral : 6.577 171.054 2564 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 2.62 % Allowed : 23.89 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2320 helix: 0.59 (0.19), residues: 796 sheet: -1.35 (0.27), residues: 355 loop : -2.30 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1441 TYR 0.013 0.001 TYR B1680 PHE 0.012 0.001 PHE A2015 TRP 0.020 0.001 TRP A2027 HIS 0.022 0.001 HIS A1924 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17939) covalent geometry : angle 0.58258 / 0.30 (24426) hydrogen bonds : bond 0.03818 / 2.58 ( 650) hydrogen bonds : angle 5.36126 / 3.83 ( 1893) Misc. bond : bond 0.00114 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 355 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9737 (tp) cc_final: 0.9475 (tp) REVERT: A 969 LEU cc_start: 0.9310 (mt) cc_final: 0.8995 (mp) REVERT: A 970 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7952 (pp) REVERT: A 972 ASP cc_start: 0.8473 (m-30) cc_final: 0.8198 (m-30) REVERT: A 994 GLU cc_start: 0.8773 (pt0) cc_final: 0.8334 (pt0) REVERT: A 1211 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7447 (m100) REVERT: A 1225 MET cc_start: 0.8877 (pmm) cc_final: 0.8575 (pmm) REVERT: A 1273 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.7291 (t70) REVERT: A 1586 ILE cc_start: 0.9150 (mp) cc_final: 0.8645 (mt) REVERT: A 1655 GLU cc_start: 0.8186 (tp30) cc_final: 0.7747 (tp30) REVERT: A 1845 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 1865 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.9189 (m-30) REVERT: A 1991 ASP cc_start: 0.9231 (t0) cc_final: 0.8945 (m-30) REVERT: A 2016 ARG cc_start: 0.9238 (mmm160) cc_final: 0.8746 (tpm170) REVERT: A 2065 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9184 (mm-30) REVERT: A 2081 LYS cc_start: 0.9667 (tppp) cc_final: 0.9424 (tppp) REVERT: B 1190 LEU cc_start: 0.9518 (mp) cc_final: 0.9201 (tp) REVERT: B 1482 MET cc_start: 0.9037 (ttp) cc_final: 0.8327 (ptm) REVERT: B 1614 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9166 (mt-10) REVERT: B 1617 GLU cc_start: 0.9301 (tt0) cc_final: 0.9065 (tm-30) outliers start: 47 outliers final: 39 residues processed: 380 average time/residue: 0.2959 time to fit residues: 175.4800 Evaluate side-chains 388 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 344 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1211 TRP Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2035 LEU Chi-restraints excluded: chain A residue 2047 ILE Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 220 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 222 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 214 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057923 restraints weight = 166590.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061372 restraints weight = 73918.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063760 restraints weight = 44861.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065372 restraints weight = 32181.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066336 restraints weight = 25668.656| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17942 Z= 0.180 Angle : 0.579 7.816 24426 Z= 0.300 Chirality : 0.040 0.175 2767 Planarity : 0.004 0.067 3244 Dihedral : 6.516 167.969 2564 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.35 % Favored : 90.47 % Rotamer: Outliers : 3.01 % Allowed : 23.89 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2320 helix: 0.49 (0.19), residues: 796 sheet: -1.45 (0.27), residues: 375 loop : -2.35 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2016 TYR 0.043 0.002 TYR B1980 PHE 0.008 0.001 PHE A1702 TRP 0.013 0.001 TRP A1998 HIS 0.007 0.001 HIS B1924 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (17939) covalent geometry : angle 0.57944 / 0.30 (24426) hydrogen bonds : bond 0.03652 / 2.48 ( 650) hydrogen bonds : angle 5.37127 / 3.82 ( 1893) Misc. bond : bond 0.00106 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 342 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9741 (tp) cc_final: 0.9485 (tp) REVERT: A 969 LEU cc_start: 0.9329 (mt) cc_final: 0.9022 (mp) REVERT: A 970 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 972 ASP cc_start: 0.8501 (m-30) cc_final: 0.8213 (m-30) REVERT: A 994 GLU cc_start: 0.8748 (pt0) cc_final: 0.7997 (pm20) REVERT: A 996 ASN cc_start: 0.8886 (t0) cc_final: 0.8676 (t0) REVERT: A 1211 TRP cc_start: 0.8335 (m100) cc_final: 0.7568 (m100) REVERT: A 1225 MET cc_start: 0.8884 (pmm) cc_final: 0.8553 (pmm) REVERT: A 1273 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.7335 (t0) REVERT: A 1424 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8437 (pp30) REVERT: A 1586 ILE cc_start: 0.9161 (mp) cc_final: 0.8652 (mt) REVERT: A 1655 GLU cc_start: 0.8241 (tp30) cc_final: 0.7843 (tp30) REVERT: A 1845 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 1991 ASP cc_start: 0.9238 (t0) cc_final: 0.8954 (m-30) REVERT: A 2065 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9193 (mm-30) REVERT: A 2081 LYS cc_start: 0.9676 (tppp) cc_final: 0.9437 (tppp) REVERT: B 1190 LEU cc_start: 0.9521 (mp) cc_final: 0.9210 (tp) REVERT: B 1482 MET cc_start: 0.9082 (ttp) cc_final: 0.8402 (ptm) REVERT: B 1614 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9173 (mt-10) REVERT: B 1617 GLU cc_start: 0.9310 (tt0) cc_final: 0.9051 (tm-30) outliers start: 54 outliers final: 47 residues processed: 373 average time/residue: 0.2880 time to fit residues: 167.8012 Evaluate side-chains 385 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1043 PHE Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1624 ASP Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2047 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1586 ILE Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 153 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 196 optimal weight: 0.0170 chunk 213 optimal weight: 5.9990 overall best weight: 2.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058190 restraints weight = 165386.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061592 restraints weight = 73913.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063917 restraints weight = 44575.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065505 restraints weight = 31820.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066474 restraints weight = 25257.578| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17942 Z= 0.181 Angle : 0.580 7.474 24426 Z= 0.304 Chirality : 0.040 0.181 2767 Planarity : 0.004 0.064 3244 Dihedral : 6.486 167.230 2564 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.61 % Favored : 90.17 % Rotamer: Outliers : 3.23 % Allowed : 23.61 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2320 helix: 0.46 (0.19), residues: 795 sheet: -1.48 (0.27), residues: 377 loop : -2.33 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2016 TYR 0.048 0.002 TYR B1980 PHE 0.011 0.001 PHE A 965 TRP 0.013 0.001 TRP A1998 HIS 0.007 0.001 HIS A1331 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (17939) covalent geometry : angle 0.58015 / 0.30 (24426) hydrogen bonds : bond 0.03608 / 2.44 ( 650) hydrogen bonds : angle 5.31447 / 3.79 ( 1893) Misc. bond : bond 0.00107 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 398 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9745 (tp) cc_final: 0.9487 (tp) REVERT: A 969 LEU cc_start: 0.9352 (mt) cc_final: 0.9040 (mp) REVERT: A 970 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 972 ASP cc_start: 0.8517 (m-30) cc_final: 0.8264 (m-30) REVERT: A 994 GLU cc_start: 0.8680 (pt0) cc_final: 0.8005 (pm20) REVERT: A 996 ASN cc_start: 0.8880 (t0) cc_final: 0.8671 (t0) REVERT: A 1211 TRP cc_start: 0.8362 (m100) cc_final: 0.7614 (m100) REVERT: A 1225 MET cc_start: 0.8890 (pmm) cc_final: 0.8562 (pmm) REVERT: A 1273 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.7319 (t70) REVERT: A 1586 ILE cc_start: 0.9181 (mp) cc_final: 0.8677 (mt) REVERT: A 1655 GLU cc_start: 0.8214 (tp30) cc_final: 0.7812 (tp30) REVERT: A 1845 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A 1865 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9198 (m-30) REVERT: A 1991 ASP cc_start: 0.9244 (t0) cc_final: 0.8959 (m-30) REVERT: A 2065 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9183 (mm-30) REVERT: A 2081 LYS cc_start: 0.9682 (tppp) cc_final: 0.9434 (tppp) REVERT: B 1190 LEU cc_start: 0.9508 (mp) cc_final: 0.9202 (tp) REVERT: B 1482 MET cc_start: 0.9109 (ttp) cc_final: 0.8447 (ptm) REVERT: B 1614 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9188 (mt-10) REVERT: B 1617 GLU cc_start: 0.9331 (tt0) cc_final: 0.9062 (tm-30) outliers start: 58 outliers final: 49 residues processed: 374 average time/residue: 0.2817 time to fit residues: 164.0564 Evaluate side-chains 387 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1045 GLU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1624 ASP Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2047 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1437 VAL Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1586 ILE Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1769 ILE Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 165 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 218 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.090004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.058390 restraints weight = 165466.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061871 restraints weight = 73302.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064290 restraints weight = 44383.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065898 restraints weight = 31790.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.066932 restraints weight = 25360.435| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17942 Z= 0.133 Angle : 0.571 7.982 24426 Z= 0.294 Chirality : 0.040 0.179 2767 Planarity : 0.004 0.053 3244 Dihedral : 6.375 166.100 2564 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.66 % Favored : 91.12 % Rotamer: Outliers : 3.01 % Allowed : 24.22 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2320 helix: 0.60 (0.19), residues: 795 sheet: -1.55 (0.26), residues: 391 loop : -2.25 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2016 TYR 0.041 0.001 TYR B1980 PHE 0.014 0.001 PHE A 965 TRP 0.012 0.001 TRP A1998 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17939) covalent geometry : angle 0.57086 / 0.29 (24426) hydrogen bonds : bond 0.03443 / 2.32 ( 650) hydrogen bonds : angle 5.17320 / 3.69 ( 1893) Misc. bond : bond 0.00125 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 397 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 343 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9739 (tp) cc_final: 0.9476 (tp) REVERT: A 969 LEU cc_start: 0.9348 (mt) cc_final: 0.9042 (mp) REVERT: A 970 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 972 ASP cc_start: 0.8465 (m-30) cc_final: 0.8231 (m-30) REVERT: A 994 GLU cc_start: 0.8666 (pt0) cc_final: 0.7988 (pm20) REVERT: A 996 ASN cc_start: 0.8845 (t0) cc_final: 0.8626 (t0) REVERT: A 1039 MET cc_start: 0.9159 (tpt) cc_final: 0.8835 (tmm) REVERT: A 1211 TRP cc_start: 0.8272 (m100) cc_final: 0.7530 (m100) REVERT: A 1225 MET cc_start: 0.8890 (pmm) cc_final: 0.8598 (pmm) REVERT: A 1273 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.7415 (t70) REVERT: A 1586 ILE cc_start: 0.9198 (mp) cc_final: 0.8710 (mt) REVERT: A 1655 GLU cc_start: 0.8192 (tp30) cc_final: 0.7809 (tp30) REVERT: A 1845 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 1991 ASP cc_start: 0.9230 (t0) cc_final: 0.8949 (m-30) REVERT: A 2081 LYS cc_start: 0.9682 (tppp) cc_final: 0.9439 (tppp) REVERT: B 1190 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9178 (tp) REVERT: B 1482 MET cc_start: 0.9041 (ttp) cc_final: 0.8377 (ptm) REVERT: B 1614 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9159 (mt-10) REVERT: B 1617 GLU cc_start: 0.9295 (tt0) cc_final: 0.9038 (tm-30) REVERT: B 1690 GLN cc_start: 0.9364 (mt0) cc_final: 0.9152 (mm-40) outliers start: 54 outliers final: 46 residues processed: 371 average time/residue: 0.2920 time to fit residues: 169.5699 Evaluate side-chains 384 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1794 LEU Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2047 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1399 LEU Chi-restraints excluded: chain B residue 1437 VAL Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1586 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1769 ILE Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 47 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 176 optimal weight: 0.0870 chunk 200 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 GLN B1640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.090195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058517 restraints weight = 166246.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062062 restraints weight = 73663.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064490 restraints weight = 44486.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.066046 restraints weight = 31772.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.067172 restraints weight = 25465.461| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17942 Z= 0.123 Angle : 0.574 7.200 24426 Z= 0.296 Chirality : 0.040 0.171 2767 Planarity : 0.004 0.050 3244 Dihedral : 6.273 164.550 2564 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 2.78 % Allowed : 24.67 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2320 helix: 0.72 (0.19), residues: 796 sheet: -1.50 (0.26), residues: 378 loop : -2.21 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2016 TYR 0.040 0.001 TYR B1980 PHE 0.014 0.001 PHE A 965 TRP 0.011 0.001 TRP A1998 HIS 0.005 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17939) covalent geometry : angle 0.57359 / 0.30 (24426) hydrogen bonds : bond 0.03377 / 2.27 ( 650) hydrogen bonds : angle 5.09505 / 3.63 ( 1893) Misc. bond : bond 0.00134 / 0.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 2060 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 LEU cc_start: 0.9741 (tp) cc_final: 0.9478 (tp) REVERT: A 969 LEU cc_start: 0.9338 (mt) cc_final: 0.9028 (mp) REVERT: A 970 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 972 ASP cc_start: 0.8495 (m-30) cc_final: 0.8283 (m-30) REVERT: A 994 GLU cc_start: 0.8636 (pt0) cc_final: 0.7977 (pm20) REVERT: A 996 ASN cc_start: 0.8863 (t0) cc_final: 0.8639 (t0) REVERT: A 1211 TRP cc_start: 0.8252 (m100) cc_final: 0.7464 (m100) REVERT: A 1225 MET cc_start: 0.8889 (pmm) cc_final: 0.8600 (pmm) REVERT: A 1273 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.7461 (t70) REVERT: A 1586 ILE cc_start: 0.9216 (mp) cc_final: 0.8682 (mt) REVERT: A 1845 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 1865 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.9216 (m-30) REVERT: A 1991 ASP cc_start: 0.9235 (t0) cc_final: 0.8940 (m-30) REVERT: A 2081 LYS cc_start: 0.9673 (tppp) cc_final: 0.9422 (tppp) REVERT: B 1190 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9167 (tp) REVERT: B 1482 MET cc_start: 0.9056 (ttp) cc_final: 0.8408 (ptm) REVERT: B 1614 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9176 (mt-10) outliers start: 50 outliers final: 42 residues processed: 371 average time/residue: 0.3050 time to fit residues: 176.1082 Evaluate side-chains 388 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1010 ARG Chi-restraints excluded: chain A residue 1032 HIS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1273 ASP Chi-restraints excluded: chain A residue 1377 GLN Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1498 HIS Chi-restraints excluded: chain A residue 1507 PHE Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1618 GLN Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1860 LEU Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1873 SER Chi-restraints excluded: chain A residue 1998 TRP Chi-restraints excluded: chain A residue 2015 PHE Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2047 ILE Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1170 LEU Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1191 LEU Chi-restraints excluded: chain B residue 1289 HIS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1347 LEU Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1379 LEU Chi-restraints excluded: chain B residue 1437 VAL Chi-restraints excluded: chain B residue 1498 HIS Chi-restraints excluded: chain B residue 1578 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1769 ILE Chi-restraints excluded: chain B residue 1870 ARG Chi-restraints excluded: chain B residue 1895 CYS Chi-restraints excluded: chain B residue 1952 GLU Chi-restraints excluded: chain B residue 1978 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1618 GLN ** A2087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.089849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058352 restraints weight = 168141.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.061890 restraints weight = 74577.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064303 restraints weight = 45009.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065915 restraints weight = 32239.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066934 restraints weight = 25722.101| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.301 17942 Z= 0.215 Angle : 0.745 59.197 24426 Z= 0.427 Chirality : 0.040 0.157 2767 Planarity : 0.004 0.048 3244 Dihedral : 6.277 164.533 2564 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.84 % Favored : 90.99 % Rotamer: Outliers : 2.67 % Allowed : 24.78 % Favored : 72.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2320 helix: 0.70 (0.19), residues: 796 sheet: -1.50 (0.26), residues: 378 loop : -2.22 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2016 TYR 0.036 0.001 TYR B1980 PHE 0.011 0.001 PHE A 965 TRP 0.011 0.001 TRP A1998 HIS 0.004 0.001 HIS A 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (17939) covalent geometry : angle 0.74519 / 0.43 (24426) hydrogen bonds : bond 0.03385 / 2.28 ( 650) hydrogen bonds : angle 5.09324 / 3.63 ( 1893) Misc. bond : bond 0.00138 / 0.07 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6999.36 seconds wall clock time: 119 minutes 52.14 seconds (7192.14 seconds total)